From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 31 Mar 2017 09:59:57 +0000 (+0100)
Subject: Merge branch 'develop' into bug/JAL-2431splitFrameNewView
X-Git-Tag: Release_2_10_3b1~336^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3d2b5edf9ea33c6ebbde4717ccc14f03554fb6f0;hp=734d0e761fda32cebaae59c370c5d64e1e8c99e8;p=jalview.git

Merge branch 'develop' into bug/JAL-2431splitFrameNewView
---

diff --git a/help/html/colourSchemes/user.html b/help/html/colourSchemes/user.html
index fb6c356..c2fde1c 100755
--- a/help/html/colourSchemes/user.html
+++ b/help/html/colourSchemes/user.html
@@ -27,7 +27,7 @@
     <strong>User Defined Colours</strong>
   </p>
   <p>
-    <img src="userDefined_java6.gif" width="815" height="402">
+    <img src="userDefined_java7.gif" width="815" height="402">
   </p>
   <p>
     You may define any number of new colour schemes, each with a unique
@@ -41,7 +41,7 @@
     The <strong>Case Sensitive</strong> option allows you to choose
     distinct colours for upper and lower case residue codes.
   <p>
-    The <strong>Lower Case Colour</strong> option allows you to apply a selected colour
+    The <strong>Colour All Lower Case	</strong> option allows you to apply a selected colour
     to all lower case residues.
   <p>
     Click <strong>Apply</strong> or <strong>OK</strong> to set your new
@@ -56,11 +56,5 @@
   <br> Any saved colour schemes will be automatically loaded the
   next time you use Jalview.
   <br>
-  <br>
-  <em>Note: the screenshot shows the appearance when running Java
-    version 6. For Java 7 (from Jalview 2.8.2) only the Swatches colour
-    chooser is currently supported (for reasons of available screen
-    space).</em>
-  <p />
 </body>
 </html>
diff --git a/help/html/colourSchemes/userDefined_java6.gif b/help/html/colourSchemes/userDefined_java6.gif
deleted file mode 100644
index d737e80..0000000
Binary files a/help/html/colourSchemes/userDefined_java6.gif and /dev/null differ
diff --git a/help/html/colourSchemes/userDefined_java7.gif b/help/html/colourSchemes/userDefined_java7.gif
index f0ced11..de80b84 100644
Binary files a/help/html/colourSchemes/userDefined_java7.gif and b/help/html/colourSchemes/userDefined_java7.gif differ
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index f720f39..f284ff9 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -68,7 +68,6 @@ action.show_gaps = Show Gaps
 action.show_hidden_markers = Show Hidden Markers
 action.find = Find
 action.undefine_groups = Undefine Groups
-action.create_groups = Create Groups
 action.make_groups_selection = Make Groups For Selection
 action.copy = Copy
 action.cut = Cut
@@ -515,7 +514,7 @@ label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences =
 label.standard_databases = Standard Databases
 label.fetch_embl_uniprot = Fetch from EMBL/EMBLCDS or Uniprot/PDB and any selected DAS sources
 label.reset_min_max_colours_to_defaults = Reset min and max colours to defaults from user preferences.
-label.align_structures_using_linked_alignment_views = Align structures using {0} linked alignment views
+label.align_structures_using_linked_alignment_views = Superpose structures using {0} selected alignment view(s)
 label.connect_to_session = Connect to session {0}
 label.threshold_feature_display_by_score = Threshold the feature display by score.
 label.threshold_feature_no_threshold = No Threshold
@@ -620,6 +619,8 @@ label.web_services = Web Services
 label.right_click_to_edit_currently_selected_parameter = Right click to edit currently selected parameter.
 label.let_jmol_manage_structure_colours = Let Jmol manage structure colours
 label.let_chimera_manage_structure_colours = Let Chimera manage structure colours
+label.fetch_chimera_attributes = Fetch Chimera attributes
+label.fetch_chimera_attributes_tip = Copy Chimera attribute to Jalview feature
 label.marks_leaves_tree_not_associated_with_sequence = Marks leaves of tree not associated with a sequence
 label.index_web_services_menu_by_host_site = Index web services in menu by the host site
 label.option_want_informed_web_service_URL_cannot_be_accessed_jalview_when_starts_up = Check this option if you want to be informed<br>when a web service URL cannot be accessed by Jalview<br>when it starts up
@@ -667,8 +668,7 @@ label.2d_rna_sequence_name = 2D RNA - {0}
 label.edit_name_and_description_current_group = Edit name and description of current group
 label.from_file = From File
 label.enter_pdb_id = Enter PDB Id (or pdbid:chaincode)
-label.text_colour = Text Colour
-action.set_text_colour = Text Colour...
+label.text_colour = Text Colour...
 label.structure = Structure
 label.show_pdbstruct_dialog = 3D Structure Data...
 label.view_rna_structure = VARNA 2D Structure
@@ -713,9 +713,14 @@ label.link_name = Link Name
 label.pdb_file = PDB file
 label.colour_with_jmol = Colour with Jmol
 label.colour_with_chimera = Colour with Chimera
-label.align_structures = Align Structures
+label.superpose_structures = Superpose Structures
+error.superposition_failed = Superposition failed: {0}
+label.insufficient_residues = Not enough aligned residues ({0}) to perform superposition
 label.jmol = Jmol
 label.chimera = Chimera
+label.create_chimera_attributes = Write Jalview features
+label.create_chimera_attributes_tip = Set Chimera residue attributes for visible features
+label.attributes_set = {0} attribute values set on Chimera
 label.sort_alignment_by_tree = Sort Alignment By Tree
 label.mark_unlinked_leaves = Mark Unlinked Leaves
 label.associate_leaves_with = Associate Leaves With
@@ -1288,4 +1293,4 @@ label.edit_sequence_url_link = Edit sequence URL link
 warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot be MIRIAM ids
 label.invalid_name = Invalid Name !
 label.output_seq_details = Output Sequence Details to list all database references
-label.urllinks = Links
\ No newline at end of file
+label.urllinks = Links
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index d408fee..a878ab7 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -66,7 +66,6 @@ action.show_gaps = Mostrar huecos
 action.show_hidden_markers = Mostrar marcadores ocultos
 action.find = Buscar
 action.undefine_groups = Grupos sin definir
-action.create_groups = Crear grupos
 action.make_groups_selection = Hacer grupos para seleccionar
 action.copy = Copiar
 action.cut = Cortar
@@ -476,7 +475,7 @@ label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences =
 label.standard_databases = Bases de datos estándar
 label.fetch_embl_uniprot = Recuperar de EMBL/EMBLCDS o Uniprot/PDB y de cualquier fuente DAS seleccionada
 label.reset_min_max_colours_to_defaults = Reiniciar los colores min y max colours a los valores por defecto establecidos en las preferencias de usuario
-label.align_structures_using_linked_alignment_views = Alinear las estructuras utlizando las {0} vistas de alineamiento enlazadas
+label.align_structures_using_linked_alignment_views = Alinear las estructuras utilizando las {0} vista(s) de alineamiento enlazada(s)
 label.connect_to_session = Conectar a la sesión {0}
 label.threshold_feature_display_by_score = Filtrar la característica mostrada por puntuación.
 label.threshold_feature_no_threshold = Sin umbral
@@ -621,7 +620,7 @@ label.2d_rna_sequence_name = 2D RNA - {0}
 label.edit_name_and_description_current_group = Editar el nombre y la descripción del grupo actual
 label.from_file = desde fichero
 label.enter_pdb_id = Introducir PDB Id
-label.text_colour = Color del texto
+label.text_colour = Color de texto...
 label.structure = Estructura
 label.create_sequence_details_report_annotation_for = Anotación para {0}
 label.sequence_details_for = Detalles de la secuencia para {0}
@@ -1158,7 +1157,6 @@ label.invalid_search=Texto de b
 action.export_annotations=Exportar Anotaciones
 action.set_as_reference=Marcar como Referencia
 action.unmark_as_reference=Desmarcar como Referencia
-action.set_text_colour=Color de Texto...
 label.chimera_failed=Error al abrir Chimera - está instalado?\nCompruebe ruta en Preferencias, Estructura
 label.find=Buscar
 label.select_pdb_file=Seleccionar Fichero PDB
@@ -1288,4 +1286,4 @@ label.edit_sequence_url_link = Editar link de secuencia URL
 warn.name_cannot_be_duplicate = Los nombres URL definidos por el usuario deben ser únicos y no pueden ser ids de MIRIAM
 label.invalid_name = Nombre inválido !
 label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas
-label.urllinks = Enlaces
\ No newline at end of file
+label.urllinks = Enlaces
diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index aac796c..3ae0650 100644
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -28,6 +28,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -577,6 +578,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     PDBChain chain;
     if (bysequence && pdb != null)
     {
@@ -604,25 +607,16 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                            sequence[s], pos);
-                  }
+                  tmp.startCol = sr.getResidueColour(sequence[s], pos,
+                          finder);
                 }
                 pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                            sequence[s], pos);
-                  }
+                  tmp.endCol = sr
+                          .getResidueColour(sequence[s], pos, finder);
                 }
-
               }
             }
           }
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 292de91..08bca8c 100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -28,6 +28,7 @@ import jalview.gui.FeatureRenderer;
 import jalview.gui.SequenceRenderer;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -546,6 +547,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
     PDBChain chain;
     if (bysequence && pdb != null)
     {
@@ -573,23 +575,15 @@ public class PDBCanvas extends JPanel implements MouseListener,
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                            sequence[s], pos);
-                  }
+                  tmp.startCol = sr.getResidueColour(sequence[s], pos,
+                          finder);
                 }
                 pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                            sequence[s], pos);
-                  }
+                  tmp.endCol = sr
+                          .getResidueColour(sequence[s], pos, finder);
                 }
 
               }
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index c40cdda..ba93046 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -39,6 +39,8 @@ import java.util.Vector;
 
 public class PDBChain
 {
+  public static final String RESNUM_FEATURE = "RESNUM";
+
   /**
    * SequenceFeature group for PDB File features added to sequences
    */
@@ -367,7 +369,7 @@ public class PDBChain
         Residue tmpres = residues.lastElement();
         Atom tmpat = tmpres.atoms.get(0);
         // Make A new SequenceFeature for the current residue numbering
-        SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+        SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName
                 + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
                 + count, offset + count, pdbid);
         resFeatures.addElement(sf);
diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 439d479..85ae718 100644
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -423,6 +423,11 @@ public class ChimeraManager
             "list selection level residue", true);
     if (chimeraReply != null)
     {
+      /*
+       * expect 0, 1 or more lines of the format
+       * residue id #0:43.A type GLY
+       * where we are only interested in the atomspec #0.43.A
+       */
       for (String inputLine : chimeraReply)
       {
         String[] inputLineParts = inputLine.split("\\s+");
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 17874e6..ee16f94 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,6 +20,10 @@
  */
 package jalview.analysis;
 
+import java.util.Arrays;
+import java.util.Hashtable;
+import java.util.List;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -37,10 +41,6 @@ import jalview.util.Format;
 import jalview.util.MappingUtils;
 import jalview.util.QuickSort;
 
-import java.util.Arrays;
-import java.util.Hashtable;
-import java.util.List;
-
 /**
  * Takes in a vector or array of sequences and column start and column end and
  * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied.
@@ -67,8 +67,8 @@ public class AAFrequency
     }
   }
 
-  public static final ProfilesI calculate(List<SequenceI> list,
-          int start, int end)
+  public static final ProfilesI calculate(List<SequenceI> list, int start,
+          int end)
   {
     return calculate(list, start, end, false);
   }
@@ -289,6 +289,56 @@ public class AAFrequency
   }
 
   /**
+   * Derive the gap count annotation row.
+   * 
+   * @param gaprow
+   *          the annotation row to add annotations to
+   * @param profiles
+   *          the source consensus data
+   * @param startCol
+   *          start column (inclusive)
+   * @param endCol
+   *          end column (exclusive)
+   */
+  public static void completeGapAnnot(AlignmentAnnotation gaprow,
+          ProfilesI profiles, int startCol, int endCol, long nseq)
+  {
+    if (gaprow == null || gaprow.annotations == null
+            || gaprow.annotations.length < endCol)
+    {
+      /*
+       * called with a bad alignment annotation row 
+       * wait for it to be initialised properly
+       */
+      return;
+    }
+    // always set ranges again
+    gaprow.graphMax = nseq;
+    gaprow.graphMin = 0;
+    for (int i = startCol; i < endCol; i++)
+    {
+      ProfileI profile = profiles.get(i);
+      if (profile == null)
+      {
+        /*
+         * happens if sequences calculated over were 
+         * shorter than alignment width
+         */
+        gaprow.annotations[i] = null;
+        return;
+      }
+
+      final int gapped = profile.getNonGapped();
+
+      String description = String.valueOf(gapped);
+
+      gaprow.annotations[i] = new Annotation(description, description,
+              '\0',
+              gapped);
+    }
+  }
+
+  /**
    * Returns a tooltip showing either
    * <ul>
    * <li>the full profile (percentages of all residues present), if
@@ -357,8 +407,7 @@ public class AAFrequency
    *          calculations
    * @return
    */
-  public static int[] extractProfile(ProfileI profile,
-          boolean ignoreGaps)
+  public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
   {
     int[] rtnval = new int[64];
     ResidueCount counts = profile.getCounts();
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index ea96b3b..232cb5d 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -42,6 +42,7 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.RangeComparator;
 import jalview.util.StringUtils;
 
 import java.io.UnsupportedEncodingException;
@@ -2265,14 +2266,7 @@ public class AlignmentUtils
      * ranges are assembled in order. Other cases should not use this method,
      * but instead construct an explicit mapping for CDS (e.g. EMBL parsing).
      */
-    Collections.sort(result, new Comparator<int[]>()
-    {
-      @Override
-      public int compare(int[] o1, int[] o2)
-      {
-        return Integer.compare(o1[0], o2[0]);
-      }
-    });
+    Collections.sort(result, new RangeComparator(true));
     return result;
   }
 
diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 2802684..8b07340 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.util.Hashtable;
@@ -46,7 +47,13 @@ import java.util.Map;
 public interface AlignViewportI extends ViewStyleI
 {
 
-  int getEndRes();
+  /**
+   * Get the ranges object containing details of the start and end sequences and
+   * residues
+   * 
+   * @return
+   */
+  public ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -119,6 +126,13 @@ public interface AlignViewportI extends ViewStyleI
   AlignmentAnnotation getAlignmentConsensusAnnotation();
 
   /**
+   * get the container for alignment gap annotation
+   * 
+   * @return
+   */
+  AlignmentAnnotation getAlignmentGapAnnotation();
+
+  /**
    * get the container for cDNA complement consensus annotation
    * 
    * @return
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index f54231e..7123b8c 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -24,6 +24,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.awt.Graphics;
 import java.util.List;
 import java.util.Map;
 
@@ -37,18 +38,32 @@ public interface FeatureRenderer
 {
 
   /**
-   * compute the perceived colour for a given column position in sequenceI,
-   * taking transparency and feature visibility into account.
+   * Computes the feature colour for a given sequence and column position,
+   * taking into account sequence feature locations, feature colour schemes,
+   * render ordering, feature and feature group visibility, and transparency.
+   * <p>
+   * The graphics argument should be provided if transparency is applied
+   * (getTransparency() < 1). With feature transparency, visible features are
+   * written to the graphics context and the composite colour may be read off
+   * from it. In this case, the returned feature colour is not the composite
+   * colour but that of the last feature drawn.
+   * <p>
+   * If no transparency applies, then the graphics argument may be null, and the
+   * returned colour is the one that would be drawn for the feature.
+   * <p>
+   * Returns null if there is no visible feature at the position.
+   * <p>
+   * This is provided to support rendering of feature colours other than on the
+   * sequence alignment, including by structure viewers and the overview window.
+   * Note this method takes no account of whether the sequence or column is
+   * hidden.
    * 
-   * @param col
-   *          - background colour (due to alignment/group shading schemes, etc).
-   * @param sequenceI
-   *          - sequence providing features
-   * @param r
-   *          - column position
+   * @param sequence
+   * @param column
+   * @param g
    * @return
    */
-  Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+  Color findFeatureColour(SequenceI sequence, int column, Graphics g);
 
   /**
    * trigger the feature discovery process for a newly created feature renderer.
@@ -170,4 +185,19 @@ public interface FeatureRenderer
    */
   void setVisible(String featureType);
 
+  /**
+   * Sets the transparency value, between 0 (full transparency) and 1 (no
+   * transparency)
+   * 
+   * @param value
+   */
+  void setTransparency(float value);
+
+  /**
+   * Returns the transparency value, between 0 (full transparency) and 1 (no
+   * transparency)
+   * 
+   * @return
+   */
+  float getTransparency();
 }
diff --git a/src/jalview/api/SequenceRenderer.java b/src/jalview/api/SequenceRenderer.java
index d708902..54f7fb6 100644
--- a/src/jalview/api/SequenceRenderer.java
+++ b/src/jalview/api/SequenceRenderer.java
@@ -21,14 +21,14 @@
 package jalview.api;
 
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 
 public interface SequenceRenderer
 {
 
-  Color getResidueBoxColour(SequenceI sequenceI, int r);
-
-  Color getResidueColour(SequenceI seq, int position, FeatureRenderer fr);
+  Color getResidueColour(SequenceI seq, int position,
+          FeatureColourFinder finder);
 
 }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 6a0b390..65c4fef 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -75,6 +75,7 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Canvas;
@@ -89,6 +90,7 @@ import java.awt.Label;
 import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.MenuItem;
+import java.awt.MenuShortcut;
 import java.awt.Panel;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
@@ -420,6 +422,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   @Override
   public void keyPressed(KeyEvent evt)
   {
+    ViewportRanges ranges = viewport.getRanges();
+
     if (viewport.cursorMode
             && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
@@ -571,8 +575,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               new String[] { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
       {
-        alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
-        alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
+        alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
+        alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
       }
       break;
 
@@ -598,8 +602,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                - viewport.endSeq + viewport.startSeq);
+        alignPanel.setScrollValues(ranges.getStartRes(),
+                2 * ranges.getStartSeq() - ranges.getEndSeq());
       }
       break;
 
@@ -610,8 +614,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                + viewport.endSeq - viewport.startSeq);
+        alignPanel
+                .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
       }
       break;
 
@@ -1068,6 +1072,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       delete_actionPerformed();
     }
+    else if (source == createGroup)
+    {
+      createGroup_actionPerformed();
+    }
+    else if (source == unGroup)
+    {
+      unGroup_actionPerformed();
+    }
     else if (source == grpsFromSelection)
     {
       makeGrpsFromSelection_actionPerformed();
@@ -2063,7 +2075,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
-    viewport.setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
     viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
@@ -2299,6 +2311,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   void trimAlignment(boolean trimLeft)
   {
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
     ColumnSelection colSel = viewport.getColumnSelection();
     int column;
 
@@ -2321,20 +2335,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       else
       {
-        seqs = viewport.getAlignment().getSequencesArray();
+        seqs = al.getSequencesArray();
       }
 
       TrimRegionCommand trimRegion;
       if (trimLeft)
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
-                column, viewport.getAlignment());
-        viewport.setStartRes(0);
+                column, al);
+        ranges.setStartRes(0);
       }
       else
       {
         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
-                column, viewport.getAlignment());
+                column, al);
       }
 
       statusBar.setText(MessageManager.formatMessage(
@@ -2343,23 +2357,25 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                       .toString() }));
       addHistoryItem(trimRegion);
 
-      for (SequenceGroup sg : viewport.getAlignment().getGroups())
+      for (SequenceGroup sg : al.getGroups())
       {
         if ((trimLeft && !sg.adjustForRemoveLeft(column))
                 || (!trimLeft && !sg.adjustForRemoveRight(column)))
         {
-          viewport.getAlignment().deleteGroup(sg);
+          al.deleteGroup(sg);
         }
       }
 
-      viewport.firePropertyChange("alignment", null, viewport
-              .getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null, al.getSequences());
     }
   }
 
   public void removeGappedColumnMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.getAlignment().getWidth() - 1;
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
+    int start = 0;
+    int end = ranges.getAbsoluteAlignmentWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -2387,22 +2403,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     // This is to maintain viewport position on first residue
     // of first sequence
-    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    SequenceI seq = al.getSequenceAt(0);
+    int startRes = seq.findPosition(ranges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
+    viewport.firePropertyChange("alignment", null, al.getSequences());
 
   }
 
   public void removeAllGapsMenuItem_actionPerformed()
   {
-    int start = 0, end = viewport.getAlignment().getWidth() - 1;
+    AlignmentI al = viewport.getAlignment();
+    ViewportRanges ranges = viewport.getRanges();
+    int start = 0;
+    int end = ranges.getAbsoluteAlignmentWidth() - 1;
 
     SequenceI[] seqs;
     if (viewport.getSelectionGroup() != null)
@@ -2419,16 +2437,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     // This is to maintain viewport position on first residue
     // of first sequence
-    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    SequenceI seq = al.getSequenceAt(0);
+    int startRes = seq.findPosition(ranges.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
-            viewport.getAlignment()));
+            al));
 
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, viewport.getAlignment()
-            .getSequences());
+    viewport.firePropertyChange("alignment", null, al.getSequences());
 
   }
 
@@ -3329,7 +3346,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(this);
     createGroup.setLabel(MessageManager.getString("action.create_group"));
+    createGroup.addActionListener(this);
     unGroup.setLabel(MessageManager.getString("action.remove_group"));
+    unGroup.addActionListener(this);
+
     annotationColumnSelection.setLabel(MessageManager
             .getString("action.select_by_annotation"));
     annotationColumnSelection.addActionListener(this);
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index fc087c6..065c503 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -35,16 +35,16 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, VamsasSource, CommandListener
+        SelectionSource
 {
   boolean cursorMode = false;
 
@@ -75,12 +75,10 @@ public class AlignViewport extends AlignmentViewport implements
     calculator = new jalview.workers.AlignCalcManager();
     this.applet = applet;
     alignment = al;
+    ranges = new ViewportRanges(this.alignment);
     // we always pad gaps
     this.setPadGaps(true);
-    this.startRes = 0;
-    this.endRes = al.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = al.getHeight() - 1;
+
     if (applet != null)
     {
       // get the width and height scaling factors if they were specified
@@ -299,7 +297,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   public void resetSeqLimits(int height)
   {
-    setEndSeq(height / getCharHeight());
+    ranges.setEndSeq(height / getCharHeight());
   }
 
   public void setCurrentTree(NJTree tree)
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index e97c347..3ae0394 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -65,6 +66,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   AnnotationLabels alabels;
 
+  ViewportRanges vpRanges;
+
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
@@ -73,6 +76,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     alignFrame = null;
     av = null;
+    vpRanges = null;
     seqPanel = null;
     seqPanelHolder = null;
     sequenceHolderPanel = null;
@@ -96,6 +100,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     seqPanel = new SeqPanel(av, this);
     idPanel = new IdPanel(av, this);
     scalePanel = new ScalePanel(av, this);
@@ -126,7 +131,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        setScrollValues(av.getStartRes(), av.getStartSeq());
+        setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
         if (getSize().height > 0
                 && annotationPanelHolder.getSize().height > 0)
         {
@@ -383,7 +388,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
        */
       if (centre)
       {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
         end = Math.min(end + offset, seq.getEnd() - 1);
       }
@@ -468,33 +473,34 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       // setScrollValues(start, seqIndex);
       // }
       // logic copied from jalview.gui.AlignmentPanel:
-      if ((startv = av.getStartRes()) >= start)
+      if ((startv = vpRanges.getStartRes()) >= start)
       {
         /*
          * Scroll left to make start of search results visible
          */
         setScrollValues(start - 1, seqIndex);
       }
-      else if ((endv = av.getEndRes()) <= end)
+      else if ((endv = vpRanges.getEndRes()) <= end)
       {
         /*
          * Scroll right to make end of search results visible
          */
         setScrollValues(startv + 1 + end - endv, seqIndex);
       }
-      else if ((starts = av.getStartSeq()) > seqIndex)
+      else if ((starts = vpRanges.getStartSeq()) > seqIndex)
       {
         /*
          * Scroll up to make start of search results visible
          */
-        setScrollValues(av.getStartRes(), seqIndex);
+        setScrollValues(vpRanges.getStartRes(), seqIndex);
       }
-      else if ((ends = av.getEndSeq()) <= seqIndex)
+      else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
       {
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+        setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -516,10 +522,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   {
     int cwidth = seqPanel.seqCanvas
             .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-    if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res <= vpRanges.getStartRes()
+            || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue(res / cwidth);
-      av.startRes = vscroll.getValue() * cwidth;
+      vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
   }
 
@@ -632,8 +639,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
   public void setWrapAlignment(boolean wrap)
   {
-    av.startSeq = 0;
-    av.startRes = 0;
+    vpRanges.setStartSeq(0);
+    vpRanges.setStartRes(0);
     scalePanelHolder.setVisible(!wrap);
 
     hscroll.setVisible(!wrap);
@@ -724,7 +731,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       x = 0;
     }
-    ;
+
 
     hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
     vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
@@ -762,17 +769,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       x = 0;
     }
 
-    av.setStartSeq(y);
-
-    int endSeq = y + vextent;
-    if (endSeq > av.getAlignment().getHeight())
-    {
-      endSeq = av.getAlignment().getHeight();
-    }
-
-    av.setEndSeq(endSeq);
-    av.setStartRes(x);
-    av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+    vpRanges.setStartSeq(y);
+    vpRanges.setEndSeq(y + vextent);
+    vpRanges.setStartRes(x);
+    vpRanges.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
             .getCharWidth())) - 1);
 
     hscroll.setValues(x, hextent, 0, width);
@@ -789,8 +789,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt == null || evt.getSource() == apvscroll)
     {
@@ -804,8 +804,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     if (evt == null || evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes(x + seqPanel.seqCanvas.getSize().width
               / av.getCharWidth() - 1);
     }
 
@@ -816,14 +816,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       {
         int rowSize = seqPanel.seqCanvas
                 .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
-        av.setStartRes(vscroll.getValue() * rowSize);
-        av.setEndRes((vscroll.getValue() + 1) * rowSize);
+        vpRanges.setStartRes(vscroll.getValue() * rowSize);
+        vpRanges.setEndRes((vscroll.getValue() + 1) * rowSize);
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
-                / av.getCharHeight());
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+                / av.getCharHeight() - 1);
       }
     }
 
@@ -832,8 +832,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
+    int scrollX = vpRanges.getStartRes() - oldX;
+    int scrollY = vpRanges.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint || av.MAC)
     {
@@ -843,13 +843,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.endRes - av.startRes)
+      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
       {
-        scrollX = av.endRes - av.startRes;
+        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
       }
-      else if (scrollX < av.startRes - av.endRes)
+      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
       {
-        scrollX = av.startRes - av.endRes;
+        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
       }
 
       idPanel.idCanvas.fastPaint(scrollY);
@@ -858,7 +858,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
       scalePanel.repaint();
       if (av.isShowAnnotation())
       {
-        annotationPanel.fastPaint(av.getStartRes() - oldX);
+        annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
       }
     }
     sendViewPosition();
@@ -955,8 +955,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
   private void sendViewPosition()
   {
     StructureSelectionManager.getStructureSelectionManager(av.applet)
-            .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
-                    av.endSeq);
+            .sendViewPosition(this, vpRanges.getStartRes(),
+                    vpRanges.getEndRes(), vpRanges.getStartSeq(),
+                    vpRanges.getEndSeq());
   }
 
   /**
@@ -1024,7 +1025,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
 
     seqPanel.seqCanvas.repaint();
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 487b75c..f516bc9 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -46,7 +46,8 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
 public class AnnotationColourChooser extends Panel implements
@@ -60,9 +61,15 @@ public class AnnotationColourChooser extends Panel implements
 
   ColourSchemeI oldcs;
 
-  Hashtable oldgroupColours;
+  Map<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  /*
+   * map from annotation to its menu item display label
+   * - so we know which item to pre-select on restore
+   */
+  private Map<AlignmentAnnotation, String> annotationLabels;
+
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 
@@ -78,17 +85,10 @@ public class AnnotationColourChooser extends Panel implements
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable();
+      oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.getColourScheme() != null)
-        {
-          oldgroupColours.put(sg, sg.getColourScheme());
-        }
-        else
-        {
-          oldgroupColours.put(sg, "null");
-        }
+        oldgroupColours.put(sg, sg.getColourScheme());
       }
     }
     this.av = av;
@@ -119,24 +119,7 @@ public class AnnotationColourChooser extends Panel implements
       // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    Vector<String> list = new Vector<String>();
-    int index = 1;
-    for (int i = 0; i < anns.length; i++)
-    {
-      String label = anns[i].label;
-      if (anns[i].sequenceRef != null)
-      {
-        label = label + "_" + anns[i].sequenceRef.getName();
-      }
-      if (!list.contains(label))
-      {
-        list.addElement(label);
-      }
-      else
-      {
-        list.addElement(label + "_" + (index++));
-      }
-    }
+    Vector<String> list = getAnnotationItems();
 
     for (int i = 0; i < list.size(); i++)
     {
@@ -153,7 +136,8 @@ public class AnnotationColourChooser extends Panel implements
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.select(acg.getAnnotation());
+      String label = annotationLabels.get(acg.getAnnotation());
+      annotations.select(label);
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
@@ -170,7 +154,7 @@ public class AnnotationColourChooser extends Panel implements
                 MessageManager
                         .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
       }
-      thresholdIsMin.setState(acg.thresholdIsMinMax);
+      thresholdIsMin.setState(acg.isThresholdIsMinMax());
       thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
@@ -186,6 +170,51 @@ public class AnnotationColourChooser extends Panel implements
     validate();
   }
 
+  /**
+   * Builds and returns a list of menu items (display text) for choice of
+   * annotation. Also builds a map between annotations and their display labels.
+   * 
+   * @return
+   */
+  protected Vector<String> getAnnotationItems()
+  {
+    // TODO remove duplication with gui.AnnotationRowFilter
+    // TODO add 'per sequence only' option / parameter
+
+    annotationLabels = new HashMap<AlignmentAnnotation, String>();
+    Vector<String> list = new Vector<String>();
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return list;
+    }
+    int index = 1;
+    for (int i = 0; i < anns.length; i++)
+    {
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        /*
+         * be helpful and include sequence id in label for
+         * sequence-associated annotation (JAL-2236)
+         */
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
+      if (!list.contains(label))
+      {
+        list.addElement(label);
+        annotationLabels.put(anns[i], label);
+      }
+      else
+      {
+        label = label + "_" + (index++);
+        list.addElement(label);
+        annotationLabels.put(anns[i], label);
+      }
+    }
+    return list;
+  }
+
   private void setDefaultMinMax()
   {
     minColour.setBackground(av.applet.getDefaultColourParameter(
@@ -501,7 +530,7 @@ public class AnnotationColourChooser extends Panel implements
       acg.setPredefinedColours(true);
     }
 
-    acg.thresholdIsMinMax = thresholdIsMin.getState();
+    acg.setThresholdIsMinMax(thresholdIsMin.getState());
 
     av.setGlobalColourScheme(acg);
 
@@ -510,7 +539,6 @@ public class AnnotationColourChooser extends Panel implements
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-
         if (sg.getColourScheme() == null)
         {
           continue;
@@ -527,7 +555,6 @@ public class AnnotationColourChooser extends Panel implements
                   currentAnnotation, minColour.getBackground(), maxColour
                           .getBackground(), aboveThreshold));
         }
-
       }
     }
 
@@ -543,20 +570,10 @@ public class AnnotationColourChooser extends Panel implements
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        Object cs = oldgroupColours.get(sg);
-        if (cs instanceof ColourSchemeI)
-        {
-          sg.setColourScheme((ColourSchemeI) cs);
-        }
-        else
-        {
-          // probably the "null" string we set it to if it was null originally.
-          sg.setColourScheme(null);
-        }
+        sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
     ap.paintAlignment(true);
-
   }
 
   @Override
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index b28ccc7..ad74b25 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -339,7 +339,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
                 av.calcPanelHeight());
         f.height += dif;
         ap.seqPanelHolder.setPreferredSize(f);
-        ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+        ap.setScrollValues(av.getRanges().getStartRes(), av.getRanges()
+                .getStartSeq());
         ap.validate();
         // ap.paintAlignment(true);
         ap.addNotify();
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 6012c1a..0ec7adf 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -462,7 +462,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth()
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -618,7 +619,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
 
     g.drawImage(image, 0, 0, this);
   }
@@ -635,7 +637,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     gg.copyArea(0, 0, imgWidth, getSize().height,
             -horizontal * av.getCharWidth(), 0);
-    int sr = av.startRes, er = av.endRes + 1, transX = 0;
+    int sr = av.getRanges().getStartRes(), er = av.getRanges().getEndRes() + 1, transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index f938cad..9b8a235 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -54,21 +54,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   public jalview.api.FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (appletJmolBinding.ap.av.isShowSequenceFeatures())
-    {
-      if (appletJmolBinding.fr == null)
-      {
-        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
-                appletJmolBinding.ap.av);
-      }
-
-      appletJmolBinding.fr
-              .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
-    }
-
-    return appletJmolBinding.fr;
+    return appletJmolBinding.ap.getFeatureRenderer();
   }
 
   @Override
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 189fe88..b369318 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -82,10 +82,10 @@ public class ExtJmol extends JalviewJmolBinding
   @Override
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
+    AlignmentPanel alignPanel = (AlignmentPanel) alignment;
+    if (alignPanel.av.isShowSequenceFeatures())
     {
-      return ap.getFeatureRenderer();
+      return alignPanel.getFeatureRenderer();
     }
     else
     {
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 67ca8e9..b88a1dc 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -377,9 +377,6 @@ public class FeatureRenderer extends
 
     if (dialog.accept)
     {
-      // This ensures that the last sequence
-      // is refreshed and new features are rendered
-      lastSeq = null;
       lastFeatureAdded = name.getText().trim();
       lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replace('\n', ' ');
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 2c454a4..1b9fbf9 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -696,8 +696,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     fr.setTransparency((100 - transparency.getValue()) / 100f);
-    ap.seqPanel.seqCanvas.repaint();
-
+    ap.paintAlignment(true);
   }
 
   class MyCheckbox extends Checkbox
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index d72e91f..abcbd70 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -103,28 +104,32 @@ public class IdCanvas extends Panel
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     gg.copyArea(0, 0, getSize().width, imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq, es = av.endSeq, transY = 0;
+    int ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transY = 0;
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+                                     // at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - vertical * av.getCharHeight();
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -180,7 +185,7 @@ public class IdCanvas extends Panel
     gg.setFont(italic);
 
     gg.fillRect(0, 0, getSize().width, getSize().height);
-    drawIds(av.startSeq, av.endSeq);
+    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
     g.drawImage(image, 0, 0, this);
   }
 
@@ -233,9 +238,10 @@ public class IdCanvas extends Panel
 
       int cHeight = alheight * avcharHeight + hgap + annotationHeight;
 
-      int rowSize = av.getEndRes() - av.getStartRes();
+      int rowSize = av.getRanges().getEndRes()
+              - av.getRanges().getStartRes();
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+      for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getSize().height)
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
@@ -263,7 +269,7 @@ public class IdCanvas extends Panel
     {
       // Now draw the id strings
       SequenceI seq;
-      for (int i = starty; i < endy; i++)
+      for (int i = starty; i <= endy; i++)
       {
 
         seq = av.getAlignment().getSequenceAt(i);
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b03a638..e47c50a 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -253,13 +253,13 @@ public class IdPanel extends Panel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+    if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && e.getY() >= getSize().height
-            && av.getAlignment().getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -398,9 +398,10 @@ public class IdPanel extends Panel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if (av.getStartSeq() > index || av.getEndSeq() < index)
+    if (av.getRanges().getStartSeq() > index
+            || av.getRanges().getEndSeq() < index)
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
     }
   }
 
@@ -431,10 +432,10 @@ public class IdPanel extends Panel implements MouseListener,
         if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 9b2be4c..3ef2936 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -20,7 +20,9 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -37,38 +39,34 @@ import java.awt.event.MouseMotionListener;
 public class OverviewPanel extends Panel implements Runnable,
         MouseMotionListener, MouseListener
 {
-  Image miniMe;
+  private OverviewDimensions od;
 
-  Image offscreen;
+  private Image miniMe;
 
-  AlignViewport av;
+  private Image offscreen;
 
-  AlignmentPanel ap;
+  private AlignViewport av;
 
-  float scalew = 1f;
+  private AlignmentPanel ap;
 
-  float scaleh = 1f;
+  private boolean resizing = false;
 
-  public int width, sequencesHeight;
-
-  int graphHeight = 20;
-
-  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
-
-  boolean resizing = false;
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  private boolean resizeAgain = false;
 
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
-  SequenceRenderer sr;
+  private SequenceRenderer sr;
 
-  FeatureRenderer fr;
+  private FeatureRenderer fr;
 
-  Frame nullFrame;
+  private Frame nullFrame;
 
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
     nullFrame = new Frame();
     nullFrame.addNotify();
@@ -79,45 +77,18 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
 
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.getAlignment().getWidth()
-            / (float) av.getAlignment().getHeight();
-
-    if (av.getSequenceConsensusHash() == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av.getSequenceConsensusHash() != null));
 
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
     {
 
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        if (getSize().width != width
-                || getSize().height != sequencesHeight + graphHeight)
+        if ((getWidth() != od.getWidth())
+                || (getHeight() != (od.getHeight())))
         {
           updateOverviewImage();
         }
@@ -155,79 +126,32 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
+    mouseAction(evt);
   }
 
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
+    mouseAction(evt);
   }
 
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    boxX = evt.getX();
-    boxY = evt.getY();
-    checkValid();
+    mouseAction(evt);
   }
 
-  void checkValid()
+  private void mouseAction(MouseEvent evt)
   {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns())
-      {
-        // Try smallest possible box
-        boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns())
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows())
-    {
-      row = av.getAlignment().getHiddenSequences()
-              .findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues(col, row);
+    od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av
+            .getRanges());
+    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 
   /**
-   * DOCUMENT ME!
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -246,27 +170,20 @@ public class OverviewPanel extends Panel implements Runnable,
 
     if ((getSize().width > 0) && (getSize().height > 0))
     {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
+      od.setWidth(getSize().width);
+      od.setHeight(getSize().height);
     }
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
 
     Thread thread = new Thread(this);
     thread.start();
     repaint();
   }
 
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
   @Override
   public void run()
   {
     miniMe = null;
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
 
     if (av.isShowSequenceFeatures())
     {
@@ -275,135 +192,37 @@ public class OverviewPanel extends Panel implements Runnable,
 
     if (getSize().width > 0 && getSize().height > 0)
     {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
+      od.setWidth(getSize().width);
+      od.setHeight(getSize().height);
     }
 
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
-    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
+    offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
 
     Graphics mg = miniMe.getGraphics();
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol = 0, lastrow = 0;
-    int xstart = 0, ystart = 0;
-    Color color = Color.yellow;
-    int row, col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI seq;
-    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
-            .hasHiddenColumns();
-    boolean hiddenRow = false;
-    AlignmentI alignment = av.getAlignment();
-    for (row = 0; row <= sequencesHeight; row++)
-    {
-      if (resizeAgain)
-      {
-        break;
-      }
-      if ((int) (row * sampleRow) == lastrow)
-      {
-        sameRow++;
-        continue;
-      }
-
-      hiddenRow = false;
-      if (hasHiddenRows)
-      {
-        seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index = alignment.getHiddenSequences()
-                  .findIndexWithoutHiddenSeqs(lastrow);
-
-          seq = alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = alignment.getSequenceAt(lastrow);
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if ((int) (col * sampleCol) == lastcol
-                && (int) (row * sampleRow) == lastrow)
-        {
-          sameCol++;
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(seq, lastcol);
-
-          if (av.isShowSequenceFeatures())
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = Color.white; // White
-        }
-
-        if (hiddenRow
-                || (hasHiddenCols && !av.getColumnSelection().isVisible(
-                        lastcol)))
-        {
-          color = color.darker().darker();
-        }
 
-        mg.setColor(color);
-        if (sameCol == 1 && sameRow == 1)
-        {
-          mg.drawLine(xstart, ystart, xstart, ystart);
-        }
-        else
-        {
-          mg.fillRect(xstart, ystart, sameCol, sameRow);
-        }
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
+    float sampleCol = alwidth / (float) od.getWidth();
+    float sampleRow = alheight / (float) od.getSequencesHeight();
 
-        xstart = col;
-        sameCol = 1;
-      }
-      lastrow = (int) (row * sampleRow);
-      ystart = row;
-      sameRow = 1;
-    }
+    buildImage(sampleRow, sampleCol, mg);
 
-    if (av.getAlignmentConservationAnnotation() != null)
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
-      for (col = 0; col < width; col++)
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
-        if (resizeAgain)
-        {
-          break;
-        }
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.renderer.drawGraph(mg,
-                  av.getAlignmentConservationAnnotation(),
-                  av.getAlignmentConservationAnnotation().annotations,
-                  (int) (sampleCol) + 1, graphHeight,
-                  (int) (col * sampleCol), (int) (col * sampleCol) + 1);
-          mg.translate(-col, -sequencesHeight);
-        }
+        mg.translate(col, od.getSequencesHeight());
+        ap.annotationPanel.renderer.drawGraph(mg,
+                av.getAlignmentConservationAnnotation(),
+                av.getAlignmentConservationAnnotation().annotations,
+                (int) (sampleCol) + 1, od.getGraphHeight(),
+                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+        mg.translate(-col, -od.getSequencesHeight());
       }
     }
     System.gc();
@@ -419,52 +238,104 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
-  public void setBoxPosition()
+  /*
+   * Build the overview panel image
+   */
+  private void buildImage(float sampleRow, float sampleCol, Graphics mg)
   {
-    int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
-            .getHiddenSequences().getSize())
-            * av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
+    int lastcol = 0;
+    int lastrow = 0;
+    int xstart = 0;
+    int ystart = 0;
+    Color color = Color.yellow;
+    int sameRow = 0;
+    int sameCol = 0;
 
-    if (av.hasHiddenColumns())
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
+    SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
+    final boolean hasHiddenCols = av.hasHiddenColumns();
+    boolean hiddenRow = false;
 
-    if (av.hasHiddenRows())
+    for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
     {
-      startSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(startSeq);
-
-      endSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(endSeq);
+      if ((int) (row * sampleRow) == lastrow)
+      {
+        sameRow++;
+      }
+      else
+      {
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // columns were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
 
+        for (int col = 0; col < od.getWidth(); col++)
+        {
+          if ((int) (col * sampleCol) == lastcol
+                  && (int) (row * sampleRow) == lastrow)
+          {
+            sameCol++;
+          }
+          else
+          {
+            lastcol = (int) (col * sampleCol);
+
+            color = getColumnColourFromSequence(seq, hiddenRow,
+                    hasHiddenCols, lastcol, finder);
+
+            mg.setColor(color);
+            if (sameCol == 1 && sameRow == 1)
+            {
+              mg.drawLine(xstart, ystart, xstart, ystart);
+            }
+            else
+            {
+              mg.fillRect(xstart, ystart, sameCol, sameRow);
+            }
+
+            xstart = col;
+            sameCol = 1;
+          }
+        }
+        lastrow = (int) (row * sampleRow);
+        ystart = row;
+        sameRow = 1;
+      }
     }
+  }
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
-
-    if (av.hasHiddenColumns())
+  /*
+   * Find the colour of a sequence at a specified column position
+   */
+  private Color getColumnColourFromSequence(
+          jalview.datamodel.SequenceI seq, boolean hiddenRow,
+          boolean hasHiddenCols, int lastcol, FeatureColourFinder finder)
+  {
+    Color color = Color.white;
+    if (seq.getLength() > lastcol)
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = sr.getResidueColour(seq, lastcol, finder);
     }
-    else
+
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = color.darker().darker();
     }
+    return color;
+  }
 
-    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
-
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   */
+  public void setBoxPosition()
+  {
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
     repaint();
   }
 
@@ -482,8 +353,7 @@ public class OverviewPanel extends Panel implements Runnable,
     {
       og.drawImage(miniMe, 0, 0, this);
       og.setColor(Color.red);
-      og.drawRect(boxX, boxY, boxWidth, boxHeight);
-      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      od.drawBox(og);
       g.drawImage(offscreen, 0, 0, this);
     }
   }
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index ed07b63..15d82a5 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -76,7 +76,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
     final int res;
 
     if (av.hasHiddenColumns())
@@ -229,7 +229,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (res > av.getAlignment().getWidth())
     {
@@ -276,7 +277,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     mouseDragging = true;
     ColumnSelection cs = av.getColumnSelection();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
     res = Math.max(0, res);
     res = cs.adjustForHiddenColumns(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
@@ -324,7 +326,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
@@ -350,7 +353,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
   @Override
   public void paint(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getSize().width,
+    drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+            getSize().width,
             getSize().height);
   }
 
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 5d6bb07..ed8a46d 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -211,17 +212,19 @@ public class SeqCanvas extends Panel
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     updateViewport();
 
     // Its possible on certain browsers that the call to fastpaint
     // is faster than it can paint, so this check here catches
     // this possibility
-    if (lastsr + horizontal != av.startRes)
+    if (lastsr + horizontal != ranges.getStartRes())
     {
-      horizontal = av.startRes - lastsr;
+      horizontal = ranges.getStartRes() - lastsr;
     }
 
-    lastsr = av.startRes;
+    lastsr = ranges.getStartRes();
 
     fastPaint = true;
     gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
@@ -229,7 +232,9 @@ public class SeqCanvas extends Panel
             imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
             -vertical * avcharHeight);
 
-    int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+    int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges
+            .getStartSeq(), es = ranges
+            .getEndSeq(), transX = 0, transY = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -244,21 +249,23 @@ public class SeqCanvas extends Panel
     else if (vertical > 0) // scroll down
     {
       ss = es - vertical;
-      if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+      if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+                                     // at a
+                                 // time
       {
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - vertical * avcharHeight;
+        transY = imgHeight - ((vertical + 1) * avcharHeight);
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -329,13 +336,16 @@ public class SeqCanvas extends Panel
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
+    ViewportRanges ranges = av.getRanges();
+
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+      drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
     }
 
     g.drawImage(img, 0, 0, this);
@@ -421,7 +431,7 @@ public class SeqCanvas extends Panel
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
@@ -610,7 +620,7 @@ public class SeqCanvas extends Panel
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
 
@@ -625,7 +635,7 @@ public class SeqCanvas extends Panel
       if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
-                + ((i - startSeq) * avcharHeight));
+                + ((i - startSeq) * avcharHeight), false);
       }
 
       // / Highlight search Results once all sequences have been drawn
@@ -694,7 +704,7 @@ public class SeqCanvas extends Panel
         int bottom = -1;
         int alHeight = av.getAlignment().getHeight() - 1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * avcharWidth;
           sy = offset + ((i - startSeq) * avcharHeight);
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 1352fe9..0e12703 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -41,6 +41,7 @@ import jalview.structure.VamsasSource;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Font;
@@ -226,16 +227,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.startSeq)
+      ViewportRanges ranges = av.getRanges();
+      while (seqCanvas.cursorY < ranges.getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
+      while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
       {
         ap.scrollUp(false);
       }
       while (seqCanvas.cursorX < av.getColumnSelection()
-              .adjustForHiddenColumns(av.startRes))
+              .adjustForHiddenColumns(ranges.getStartRes()))
       {
 
         if (!ap.scrollRight(false))
@@ -244,7 +246,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
       }
       while (seqCanvas.cursorX > av.getColumnSelection()
-              .adjustForHiddenColumns(av.endRes))
+              .adjustForHiddenColumns(ranges.getEndRes()))
       {
         if (!ap.scrollRight(true))
         {
@@ -624,14 +626,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getStartRes() / cwidth;
+      wrappedBlock += av.getRanges().getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
     }
     else
     {
-      res = (x / av.getCharWidth()) + av.getStartRes();
+      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
     }
 
     if (av.hasHiddenColumns())
@@ -681,7 +683,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+      seq = Math.min((y / av.getCharHeight())
+              + av.getRanges().getStartSeq(),
+              av
               .getAlignment().getHeight() - 1);
       if (seq < 0)
       {
@@ -1643,8 +1647,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       oldSeq = -1;
     }
 
-    if (res > av.endRes || res < av.startRes || y < av.startSeq
-            || y > av.endSeq)
+    if (res > av.getRanges().getEndRes()
+            || res < av.getRanges().getStartRes()
+            || y < av.getRanges().getStartSeq()
+            || y > av.getRanges().getEndSeq())
     {
       mouseExited(evt);
     }
@@ -1742,13 +1748,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         if (evt != null)
         {
 
-          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+          if (mouseDragging && evt.getY() < 0
+                  && av.getRanges().getStartSeq() > 0)
           {
             running = ap.scrollUp(true);
           }
 
           if (mouseDragging && evt.getY() >= getSize().height
-                  && av.getAlignment().getHeight() > av.getEndSeq())
+                  && av.getAlignment().getHeight() > av.getRanges()
+                          .getEndSeq())
           {
             running = ap.scrollUp(false);
           }
@@ -1890,8 +1898,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollTo(int row, int column)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    column = column < 0 ? ap.av.startRes : column;
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
     ap.scrollTo(column, column, row, true, true);
   }
 
@@ -1903,8 +1911,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToRow(int row)
   {
 
-    row = row < 0 ? ap.av.startSeq : row;
-    ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+    row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+    ap.scrollTo(ap.av.getRanges().getStartRes(), ap.av.getRanges()
+            .getStartRes(), row, true, true);
   }
 
   /**
@@ -1915,8 +1924,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   public void scrollToColumn(int column)
   {
 
-    column = column < 0 ? ap.av.startRes : column;
-    ap.scrollTo(column, column, ap.av.startSeq, true, true);
+    column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+    ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true, true);
   }
 
   /**
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 86d1f98..78ed4a3 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -20,10 +20,10 @@
  */
 package jalview.appletgui;
 
-import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 
 import java.awt.Color;
 import java.awt.Font;
@@ -69,8 +69,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     this.renderGaps = renderGaps;
   }
 
-  @Override
-  public Color getResidueBoxColour(SequenceI seq, int i)
+  protected Color getResidueBoxColour(SequenceI seq, int i)
   {
     allGroups = av.getAlignment().findAllGroups(seq);
 
@@ -96,20 +95,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * 
    * @param seq
    * @param position
-   * @param fr
+   * @param finder
    * @return
    */
   @Override
   public Color getResidueColour(final SequenceI seq, int position,
-          FeatureRenderer fr)
+          FeatureColourFinder finder)
   {
     // TODO replace 8 or so code duplications with calls to this method
     // (refactored as needed)
     Color col = getResidueBoxColour(seq, position);
 
-    if (fr != null)
+    if (finder != null)
     {
-      col = fr.findFeatureColour(col, seq, position);
+      col = finder.findFeatureColour(col, seq, position);
     }
     return col;
   }
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 48c1ee9..da3cb92 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import jalview.datamodel.PDBEntry;
 import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
@@ -1037,7 +1038,7 @@ public class Cache
       String file = st.nextToken();
       try
       {
-        UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+        UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
         if (ucs != null)
         {
           if (coloursFound.length() > 0)
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index a6f2bf4..41488ea 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -185,14 +185,7 @@ public class Alignment implements AlignmentI
     return AlignmentUtils.getSequencesByName(this);
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public SequenceI getSequenceAt(int i)
   {
@@ -206,6 +199,28 @@ public class Alignment implements AlignmentI
     return null;
   }
 
+  @Override
+  public SequenceI getSequenceAtAbsoluteIndex(int i)
+  {
+    SequenceI seq = null;
+    if (getHiddenSequences().getSize() > 0)
+    {
+      seq = getHiddenSequences().getHiddenSequence(i);
+      if (seq == null)
+      {
+        // didn't find the sequence in the hidden sequences, get it from the
+        // alignment
+        int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+        seq = getSequenceAt(index);
+      }
+    }
+    else
+    {
+      seq = getSequenceAt(i);
+    }
+    return seq;
+  }
+
   /**
    * Adds a sequence to the alignment. Recalculates maxLength and size. Note
    * this currently does not recalculate whether or not the alignment is
@@ -320,30 +335,21 @@ public class Alignment implements AlignmentI
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(SequenceI s)
   {
-    deleteSequence(findIndex(s));
+    synchronized (sequences)
+    {
+      deleteSequence(findIndex(s));
+    }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   */
   @Override
   public void deleteSequence(int i)
   {
-    if (i > -1 && i < getHeight())
+    synchronized (sequences)
     {
-      synchronized (sequences)
+      if (i > -1 && i < getHeight())
       {
         sequences.remove(i);
         hiddenSequences.adjustHeightSequenceDeleted(i);
@@ -351,6 +357,18 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public void deleteHiddenSequence(int i)
+  {
+    synchronized (sequences)
+    {
+      if (i > -1 && i < getHeight())
+      {
+        sequences.remove(i);
+      }
+    }
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -668,22 +686,19 @@ public class Alignment implements AlignmentI
     return -1;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+
   @Override
   public int getHeight()
   {
     return sequences.size();
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
+  @Override
+  public int getAbsoluteHeight()
+  {
+    return sequences.size() + getHiddenSequences().getSize();
+  }
+
   @Override
   public int getWidth()
   {
@@ -769,6 +784,12 @@ public class Alignment implements AlignmentI
     return true;
   }
 
+  @Override
+  public boolean isHidden(int alignmentIndex)
+  {
+    return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+  }
+
   /**
    * Delete all annotations, including auto-calculated if the flag is set true.
    * Returns true if at least one annotation was deleted, else false.
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 05688cb..6117baf 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -20,10 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.Rna;
-import jalview.analysis.SecStrConsensus.SimpleBP;
-import jalview.analysis.WUSSParseException;
-
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
@@ -32,6 +28,10 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 
+import jalview.analysis.Rna;
+import jalview.analysis.SecStrConsensus.SimpleBP;
+import jalview.analysis.WUSSParseException;
+
 /**
  * DOCUMENT ME!
  * 
@@ -170,10 +170,14 @@ public class AlignmentAnnotation
    */
   private Map<Integer, Annotation> sequenceMapping;
 
-  /** DOCUMENT ME!! */
+  /**
+   * lower range for quantitative data
+   */
   public float graphMin;
 
-  /** DOCUMENT ME!! */
+  /**
+   * Upper range for quantitative data
+   */
   public float graphMax;
 
   /**
@@ -863,6 +867,10 @@ public class AlignmentAnnotation
   @Override
   public String toString()
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuilder buffer = new StringBuilder(256);
 
     for (int i = 0; i < annotations.length; i++)
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5d185cd..2abb1f8 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -31,13 +31,22 @@ import java.util.Set;
 public interface AlignmentI extends AnnotatedCollectionI
 {
   /**
-   * Calculates the number of sequences in an alignment
+   * Calculates the number of sequences in an alignment, excluding hidden
+   * sequences
    * 
    * @return Number of sequences in alignment
    */
   int getHeight();
 
   /**
+   * Calculates the number of sequences in an alignment, including hidden
+   * sequences
+   * 
+   * @return Number of sequences in alignment
+   */
+  int getAbsoluteHeight();
+
+  /**
    * 
    * Calculates the maximum width of the alignment, including gaps.
    * 
@@ -65,6 +74,15 @@ public interface AlignmentI extends AnnotatedCollectionI
   boolean isAligned(boolean includeHidden);
 
   /**
+   * Answers if the sequence at alignmentIndex is hidden
+   * 
+   * @param alignmentIndex
+   *          the index to check
+   * @return true if the sequence is hidden
+   */
+  boolean isHidden(int alignmentIndex);
+
+  /**
    * Gets sequences as a Synchronized collection
    * 
    * @return All sequences in alignment.
@@ -90,6 +108,17 @@ public interface AlignmentI extends AnnotatedCollectionI
   SequenceI getSequenceAt(int i);
 
   /**
+   * Find a specific sequence in this alignment.
+   * 
+   * @param i
+   *          Index of required sequence in full alignment, i.e. if all columns
+   *          were visible
+   * 
+   * @return SequenceI at given index.
+   */
+  SequenceI getSequenceAtAbsoluteIndex(int i);
+
+  /**
    * Returns a map of lists of sequences keyed by sequence name.
    * 
    * @return
@@ -118,7 +147,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   SequenceI replaceSequenceAt(int i, SequenceI seq);
 
   /**
-   * Deletes a sequence from the alignment
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param s
    *          Sequence to be deleted.
@@ -126,7 +157,9 @@ public interface AlignmentI extends AnnotatedCollectionI
   void deleteSequence(SequenceI s);
 
   /**
-   * Deletes a sequence from the alignment.
+   * Deletes a sequence from the alignment. Updates hidden sequences to account
+   * for the removed sequence. Do NOT use this method to delete sequences which
+   * are just hidden.
    * 
    * @param i
    *          Index of sequence to be deleted.
@@ -134,6 +167,14 @@ public interface AlignmentI extends AnnotatedCollectionI
   void deleteSequence(int i);
 
   /**
+   * Deletes a sequence in the alignment which has been hidden.
+   * 
+   * @param i
+   *          Index of sequence to be deleted
+   */
+  void deleteHiddenSequence(int i);
+
+  /**
    * Finds sequence in alignment using sequence name as query.
    * 
    * @param name
@@ -545,4 +586,5 @@ public interface AlignmentI extends AnnotatedCollectionI
    * @return
    */
   public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
 }
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 98a7fe2..97bc5a3 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -690,8 +690,8 @@ public class ColumnSelection
    * left-most visible column will always be returned.
    * 
    * @param hiddenColumn
-   *          int
-   * @return int
+   *          the column index in the full alignment including hidden columns
+   * @return the position of the column in the visible alignment
    */
   public int findColumnPosition(int hiddenColumn)
   {
@@ -708,15 +708,89 @@ public class ColumnSelection
           result -= region[1] + 1 - region[0];
         }
       } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
-      if (hiddenColumn > region[0] && hiddenColumn < region[1])
-      {
-        return region[0] + hiddenColumn - result;
+
+      if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+       {
+         // Here the hidden column is within a region, so
+         // we want to return the position of region[0]-1, adjusted for any
+         // earlier hidden columns.
+         // Calculate the difference between the actual hidden col position
+         // and region[0]-1, and then subtract from result to convert result from
+         // the adjusted hiddenColumn value to the adjusted region[0]-1 value
+
+        // However, if the region begins at 0 we cannot return region[0]-1
+        // just return 0
+        if (region[0] == 0)
+        {
+          return 0;
+        }
+        else
+        {
+          return result - (hiddenColumn - region[0] + 1);
+        }
       }
     }
     return result; // return the shifted position after removing hidden columns.
   }
 
   /**
+   * Find the visible column which is a given visible number of columns to the
+   * left of another visible column. i.e. for a startColumn x, the column which
+   * is distance 1 away will be column x-1.
+   * 
+   * @param visibleDistance
+   *          the number of visible columns to offset by
+   * @param startColumn
+   *          the column to start from
+   * @return the position of the column in the visible alignment
+   */
+  public int subtractVisibleColumns(int visibleDistance, int startColumn)
+  {
+    int distance = visibleDistance;
+
+    // in case startColumn is in a hidden region, move it to the left
+    int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+
+    // get index of hidden region to left of start
+    int index = getHiddenIndexLeft(start);
+    if (index == -1)
+    {
+      // no hidden regions to left of startColumn
+      return start - distance;
+    }
+
+    // walk backwards through the alignment subtracting the counts of visible
+    // columns from distance
+    int[] region;
+    int gap = 0;
+    int nextstart = start;
+
+    while ((index > -1) && (distance - gap > 0))
+    {
+      // subtract the gap to right of region from distance
+      distance -= gap;
+      start = nextstart;
+
+      // calculate the next gap
+      region = hiddenColumns.get(index);
+      gap = start - region[1];
+
+      // set start to just to left of current region
+      nextstart = region[0] - 1;
+      index--;
+    }
+
+    if (distance - gap > 0)
+    {
+      // fell out of loop because there are no more hidden regions
+      distance -= gap;
+      return nextstart - distance;
+    }
+    return start - distance;
+
+  }
+
+  /**
    * Use this method to determine where the next hiddenRegion starts
    * 
    * @param hiddenRegion
@@ -805,6 +879,35 @@ public class ColumnSelection
 
   }
 
+  /**
+   * This method returns the index of the hidden region to the left of a column
+   * position. If the column is in a hidden region it returns the index of the
+   * region to the left. If there is no hidden region to the left it returns -1.
+   * 
+   * @param pos
+   *          int
+   */
+  private int getHiddenIndexLeft(int pos)
+  {
+    if (hiddenColumns != null)
+    {
+      int index = hiddenColumns.size() - 1;
+      do
+      {
+        int[] region = hiddenColumns.elementAt(index);
+        if (pos > region[1])
+        {
+          return index;
+        }
+
+        index--;
+      } while (index > -1);
+    }
+
+    return -1;
+
+  }
+
   public void hideSelectedColumns()
   {
     synchronized (selection)
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 9e2cf72..6950c28 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -154,8 +154,8 @@ public class HiddenSequences
       hiddenSequences = new SequenceI[alignment.getHeight()];
     }
 
-    int alignmentIndex = alignment.findIndex(sequence);
-    alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+    int absAlignmentIndex = alignment.findIndex(sequence);
+    int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
 
     if (hiddenSequences[alignmentIndex] != null)
     {
@@ -164,7 +164,7 @@ public class HiddenSequences
 
     hiddenSequences[alignmentIndex] = sequence;
 
-    alignment.deleteSequence(sequence);
+    alignment.deleteHiddenSequence(absAlignmentIndex);
   }
 
   public List<SequenceI> showAll(
@@ -246,6 +246,12 @@ public class HiddenSequences
     return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
   }
 
+  /**
+   * Convert absolute alignment index to visible alignment index
+   * 
+   * @param alignmentIndex
+   * @return
+   */
   public int findIndexWithoutHiddenSeqs(int alignmentIndex)
   {
     if (hiddenSequences == null)
@@ -254,8 +260,14 @@ public class HiddenSequences
     }
     int index = 0;
     int hiddenSeqs = 0;
+    int diff = 0;
     if (hiddenSequences.length <= alignmentIndex)
     {
+      // if the alignmentIndex runs past the end of hidden sequences
+      // and therefore actually past the end of the alignment
+      // store the difference to add back on at the end, so that behaviour
+      // is consistent with hidden columns behaviour (used by overview panel)
+      diff = alignmentIndex - hiddenSequences.length + 1;
       alignmentIndex = hiddenSequences.length - 1;
     }
 
@@ -268,9 +280,50 @@ public class HiddenSequences
       index++;
     }
 
-    return (alignmentIndex - hiddenSeqs);
+    return (alignmentIndex - hiddenSeqs + diff);
+  }
+
+  /**
+   * Find the visible row which is a given visible number of rows above another
+   * visible row. i.e. for a startRow x, the row which is distance 1 away will
+   * be row x-1.
+   * 
+   * @param visibleDistance
+   *          the number of visible rows to offset by
+   * @param startRow
+   *          the row to start from
+   * @return the position of the row in the visible alignment
+   */
+  public int subtractVisibleRows(int visibleDistance, int startRow)
+  {
+    // walk upwards through the alignment
+    // count all the non-null sequences until we have visibleDistance counted
+    // then return the next visible sequence
+    if (hiddenSequences == null)
+    {
+      return startRow - visibleDistance;
+    }
+
+    int index = startRow;
+    int count = 0;
+    while ((index > -1) && (count < visibleDistance))
+    {
+      if (hiddenSequences[index] == null)
+      {
+        // count visible sequences
+        count++;
+      }
+      index--;
+    }
+    return index;
   }
 
+  /**
+   * Convert alignment index from visible alignment to absolute alignment
+   * 
+   * @param alignmentIndex
+   * @return
+   */
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     if (hiddenSequences == null)
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c8b94ce..b0faf21 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -314,12 +314,11 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public synchronized void addSequenceFeature(SequenceFeature sf)
+  public synchronized boolean addSequenceFeature(SequenceFeature sf)
   {
     if (sequenceFeatures == null && datasetSequence != null)
     {
-      datasetSequence.addSequenceFeature(sf);
-      return;
+      return datasetSequence.addSequenceFeature(sf);
     }
     if (sequenceFeatures == null)
     {
@@ -330,7 +329,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       if (sequenceFeatures[i].equals(sf))
       {
-        return;
+        return false;
       }
     }
 
@@ -339,6 +338,7 @@ public class Sequence extends ASequence implements SequenceI
     temp[sequenceFeatures.length] = sf;
 
     sequenceFeatures = temp;
+    return true;
   }
 
   @Override
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index aec68ab..92f797f 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -337,7 +337,14 @@ public interface SequenceI extends ASequenceI
    */
   public void addDBRef(DBRefEntry entry);
 
-  public void addSequenceFeature(SequenceFeature sf);
+  /**
+   * Adds the given sequence feature and returns true, or returns false if it is
+   * already present on the sequence
+   * 
+   * @param sf
+   * @return
+   */
+  public boolean addSequenceFeature(SequenceFeature sf);
 
   public void deleteFeature(SequenceFeature sf);
 
diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 732bc0f..233707b 100644
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -38,6 +38,7 @@ import jalview.io.gff.SequenceOntologyI;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
+import jalview.util.RangeComparator;
 
 import java.io.IOException;
 import java.net.MalformedURLException;
@@ -110,26 +111,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   }
 
   /**
-   * A comparator to sort ranges into ascending start position order
-   */
-  private class RangeSorter implements Comparator<int[]>
-  {
-    boolean forwards;
-
-    RangeSorter(boolean forward)
-    {
-      forwards = forward;
-    }
-
-    @Override
-    public int compare(int[] o1, int[] o2)
-    {
-      return (forwards ? 1 : -1) * Integer.compare(o1[0], o2[0]);
-    }
-
-  }
-
-  /**
    * Default constructor (to use rest.ensembl.org)
    */
   public EnsemblSeqProxy()
@@ -626,7 +607,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      * a final sort is needed since Ensembl returns CDS sorted within source
      * (havana / ensembl_havana)
      */
-    Collections.sort(regions, new RangeSorter(direction == 1));
+    Collections.sort(regions, new RangeComparator(direction == 1));
 
     List<int[]> to = Arrays.asList(new int[] { start,
         start + mappedLength - 1 });
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index bf80831..94df99a 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.jmol;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -34,6 +35,7 @@ import jalview.structure.AtomSpec;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -43,6 +45,7 @@ import java.io.File;
 import java.net.URL;
 import java.security.AccessControlException;
 import java.util.ArrayList;
+import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -227,21 +230,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   /**
-   * Construct and send a command to align structures against a reference
-   * structure, based on one or more sequence alignments
-   * 
-   * @param _alignment
-   *          an array of alignments to process
-   * @param _refStructure
-   *          an array of corresponding reference structures (index into pdb
-   *          file array); if a negative value is passed, the first PDB file
-   *          mapped to an alignment sequence is used as the reference for
-   *          superposition
-   * @param _hiddenCols
-   *          an array of corresponding hidden columns for each alignment
+   * {@inheritDoc}
    */
   @Override
-  public void superposeStructures(AlignmentI[] _alignment,
+  public String superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
     while (viewer.isScriptExecuting())
@@ -261,7 +253,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     String[] files = getPdbFile();
     if (!waitForFileLoad(files))
     {
-      return;
+      return null;
     }
 
     StringBuilder selectioncom = new StringBuilder(256);
@@ -277,6 +269,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       nSeconds = " " + (2.0 / files.length) + " ";
       // if (nSeconds).substring(0,5)+" ";
     }
+
     // see JAL-1345 - should really automatically turn off the animation for
     // large numbers of structures, but Jmol doesn't seem to allow that.
     // nSeconds = " ";
@@ -302,14 +295,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
 
       /*
-       * 'matched' array will hold 'true' for visible alignment columns where
+       * 'matched' bit j will be set for visible alignment columns j where
        * all sequences have a residue with a mapping to the PDB structure
        */
-      // TODO could use a BitSet for matched
-      boolean matched[] = new boolean[alignment.getWidth()];
-      for (int m = 0; m < matched.length; m++)
+      BitSet matched = new BitSet();
+      for (int m = 0; m < alignment.getWidth(); m++)
       {
-        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+        if (hiddenCols == null || hiddenCols.isVisible(m))
+        {
+          matched.set(m);
+        }
       }
 
       SuperposeData[] structures = new SuperposeData[files.length];
@@ -334,17 +329,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
 
       String[] selcom = new String[files.length];
-      int nmatched = 0;
-      for (boolean b : matched)
-      {
-        if (b)
-        {
-          nmatched++;
-        }
-      }
+      int nmatched = matched.cardinality();
       if (nmatched < 4)
       {
-        // TODO: bail out here because superposition illdefined?
+        return (MessageManager.formatMessage(
+"label.insufficient_residues",
+                nmatched));
       }
 
       /*
@@ -359,35 +349,35 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           boolean run = false;
           StringBuilder molsel = new StringBuilder();
           molsel.append("{");
-          for (int r = 0; r < matched.length; r++)
+
+          int nextColumnMatch = matched.nextSetBit(0);
+          while (nextColumnMatch != -1)
           {
-            if (matched[r])
+            int pdbResNo = structures[pdbfnum].pdbResNo[nextColumnMatch];
+            if (lpos != pdbResNo - 1)
             {
-              int pdbResNo = structures[pdbfnum].pdbResNo[r];
-              if (lpos != pdbResNo - 1)
+              // discontinuity
+              if (lpos != -1)
               {
-                // discontinuity
-                if (lpos != -1)
-                {
-                  molsel.append(lpos);
-                  molsel.append(chainCd);
-                  molsel.append("|");
-                }
-                run = false;
+                molsel.append(lpos);
+                molsel.append(chainCd);
+                molsel.append("|");
               }
-              else
+              run = false;
+            }
+            else
+            {
+              // continuous run - and lpos >-1
+              if (!run)
               {
-                // continuous run - and lpos >-1
-                if (!run)
-                {
-                  // at the beginning, so add dash
-                  molsel.append(lpos);
-                  molsel.append("-");
-                }
-                run = true;
+                // at the beginning, so add dash
+                molsel.append(lpos);
+                molsel.append("-");
               }
-              lpos = pdbResNo;
+              run = true;
             }
+            lpos = pdbResNo;
+            nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
           }
           /*
            * add final selection phrase
@@ -473,6 +463,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
               + selectioncom.toString() + "); cartoons; ");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
     }
+
+    return null;
   }
 
   public void evalStateCommand(String command)
@@ -507,17 +499,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * @param files
    * @param sr
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, alignment);
+            getSequence(), sr, viewPanel);
   }
 
   /**
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index d5676c5..23e0a6f 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -20,16 +20,21 @@
  */
 package jalview.ext.jmol;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Routines for generating Jmol commands for Jalview/Jmol binding another
@@ -50,11 +55,15 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
-
-    ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
+    ColumnSelection cs = viewport.getColumnSelection();
+    AlignmentI al = viewport.getAlignment();
+    List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
 
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
@@ -74,9 +83,9 @@ public class JmolCommands
         for (int sp, m = 0; m < mapping.length; m++)
         {
           if (mapping[m].getSequence() == sequence[pdbfnum][s]
-                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+                  && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
           {
-            SequenceI asp = alignment.getSequenceAt(sp);
+            SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
               // no mapping to gaps in sequence
@@ -93,12 +102,17 @@ public class JmolCommands
 
               lastPos = pos;
 
-              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+              Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+                      finder);
 
-              if (fr != null)
+              /*
+               * shade hidden regions darker
+               */
+              if (!cs.isVisible(r))
               {
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+                col = Color.GRAY;
               }
+
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                       + "/"
diff --git a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
new file mode 100644
index 0000000..d62cc3c
--- /dev/null
+++ b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
@@ -0,0 +1,180 @@
+package jalview.ext.rbvi.chimera;
+
+import jalview.util.RangeComparator;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+/**
+ * A class to model a Chimera atomspec pattern, for example
+ * 
+ * <pre>
+ * #0:15.A,28.A,54.A,63.A,70-72.A,83-84.A,97-98.A|#1:2.A,6.A,11.A,13-14.A,70.A,82.A,96-97.A
+ * </pre>
+ * 
+ * where
+ * <ul>
+ * <li>#0 is a model number</li>
+ * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
+ * <li>.A is a chain identifier</li>
+ * <li>residue ranges are separated by comma</li>
+ * <li>atomspecs for distinct models are separated by | (or)</li>
+ * </ul>
+ * 
+ * <pre>
+ * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ * </pre>
+ */
+public class AtomSpecModel
+{
+  private Map<Integer, Map<String, List<int[]>>> atomSpec;
+
+  /**
+   * Constructor
+   */
+  public AtomSpecModel()
+  {
+    atomSpec = new TreeMap<Integer, Map<String, List<int[]>>>();
+  }
+
+  /**
+   * Adds one contiguous range to this atom spec
+   * 
+   * @param model
+   * @param startPos
+   * @param endPos
+   * @param chain
+   */
+  public void addRange(int model, int startPos, int endPos, String chain)
+  {
+    /*
+     * Get/initialize map of data for the colour and model
+     */
+    Map<String, List<int[]>> modelData = atomSpec.get(model);
+    if (modelData == null)
+    {
+      atomSpec.put(model, modelData = new TreeMap<String, List<int[]>>());
+    }
+
+    /*
+     * Get/initialize map of data for colour, model and chain
+     */
+    List<int[]> chainData = modelData.get(chain);
+    if (chainData == null)
+    {
+      chainData = new ArrayList<int[]>();
+      modelData.put(chain, chainData);
+    }
+
+    /*
+     * Add the start/end positions
+     */
+    chainData.add(new int[] { startPos, endPos });
+    // TODO add intelligently, using a RangeList class
+  }
+
+  /**
+   * Returns the range(s) formatted as a Chimera atomspec
+   * 
+   * @return
+   */
+  public String getAtomSpec()
+  {
+    StringBuilder sb = new StringBuilder(128);
+    boolean firstModel = true;
+    for (Integer model : atomSpec.keySet())
+    {
+      if (!firstModel)
+      {
+        sb.append("|");
+      }
+      firstModel = false;
+      sb.append("#").append(model).append(":");
+
+      boolean firstPositionForModel = true;
+      final Map<String, List<int[]>> modelData = atomSpec.get(model);
+
+      for (String chain : modelData.keySet())
+      {
+        chain = chain.trim();
+
+        List<int[]> rangeList = modelData.get(chain);
+
+        /*
+         * sort ranges into ascending start position order
+         */
+        Collections.sort(rangeList, new RangeComparator(true));
+
+        int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0];
+        int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1];
+
+        Iterator<int[]> iterator = rangeList.iterator();
+        while (iterator.hasNext())
+        {
+          int[] range = iterator.next();
+          if (range[0] <= end + 1)
+          {
+            /*
+             * range overlaps or is contiguous with the last one
+             * - so just extend the end position, and carry on
+             * (unless this is the last in the list)
+             */
+            end = Math.max(end, range[1]);
+          }
+          else
+          {
+            /*
+             * we have a break so append the last range
+             */
+            appendRange(sb, start, end, chain, firstPositionForModel);
+            firstPositionForModel = false;
+            start = range[0];
+            end = range[1];
+          }
+        }
+
+        /*
+         * and append the last range
+         */
+        if (!rangeList.isEmpty())
+        {
+          appendRange(sb, start, end, chain, firstPositionForModel);
+          firstPositionForModel = false;
+        }
+      }
+    }
+    return sb.toString();
+  }
+
+  /**
+   * @param sb
+   * @param start
+   * @param end
+   * @param chain
+   * @param firstPositionForModel
+   */
+  protected void appendRange(StringBuilder sb, int start, int end,
+          String chain, boolean firstPositionForModel)
+  {
+    if (!firstPositionForModel)
+    {
+      sb.append(",");
+    }
+    if (end == start)
+    {
+      sb.append(start);
+    }
+    else
+    {
+      sb.append(start).append("-").append(end);
+    }
+    if (chain.length() > 0)
+    {
+      sb.append(".").append(chain);
+    }
+  }
+}
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 8f6b2f1..95757fd 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,10 +20,15 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
@@ -32,11 +37,10 @@ import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
 
 /**
  * Routines for generating Chimera commands for Jalview/Chimera binding
@@ -47,26 +51,32 @@ import java.util.TreeMap;
 public class ChimeraCommands
 {
 
+  public static final String NAMESPACE_PREFIX = "jv_";
+
   /**
-   * utility to construct the commands to colour chains by the given alignment
-   * for passing to Chimera
-   * 
-   * @returns Object[] { Object[] { <model being coloured>,
+   * Constructs Chimera commands to colour residues as per the Jalview alignment
    * 
+   * @param ssm
+   * @param files
+   * @param sequence
+   * @param sr
+   * @param fr
+   * @param viewPanel
+   * @return
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
-    Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
-            ssm, files, sequence, sr, fr, alignment);
+    Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+            sequence, sr, viewPanel);
 
     List<String> colourCommands = buildColourCommands(colourMap);
 
     StructureMappingcommandSet cs = new StructureMappingcommandSet(
             ChimeraCommands.class, null,
-            colourCommands.toArray(new String[0]));
+            colourCommands.toArray(new String[colourCommands.size()]));
 
     return new StructureMappingcommandSet[] { cs };
   }
@@ -76,18 +86,18 @@ public class ChimeraCommands
    * 'color' commands (one per distinct colour used). The format of each command
    * is
    * 
-   * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
-   * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
-   * 
-   * @see http 
-   *      ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
-   *      .html </pre>
+   * <pre>
+   * <blockquote> 
+   * color colorname #modelnumber:range.chain 
+   * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+   * </blockquote>
+   * </pre>
    * 
    * @param colourMap
    * @return
    */
   protected static List<String> buildColourCommands(
-          Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap)
+          Map<Object, AtomSpecModel> colourMap)
   {
     /*
      * This version concatenates all commands into a single String (semi-colon
@@ -97,8 +107,9 @@ public class ChimeraCommands
     List<String> commands = new ArrayList<String>();
     StringBuilder sb = new StringBuilder(256);
     boolean firstColour = true;
-    for (Color colour : colourMap.keySet())
+    for (Object key : colourMap.keySet())
     {
+      Color colour = (Color) key;
       String colourCode = ColorUtils.toTkCode(colour);
       if (!firstColour)
       {
@@ -106,55 +117,68 @@ public class ChimeraCommands
       }
       sb.append("color ").append(colourCode).append(" ");
       firstColour = false;
-      boolean firstModelForColour = true;
-      final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
-              .get(colour);
-      for (Integer model : colourData.keySet())
+      final AtomSpecModel colourData = colourMap.get(colour);
+      sb.append(colourData.getAtomSpec());
+    }
+    commands.add(sb.toString());
+    return commands;
+  }
+
+  /**
+   * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
+   * builds a Chimera format atom spec
+   * 
+   * @param modelAndChainRanges
+   */
+  protected static String getAtomSpec(
+          Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
+  {
+    StringBuilder sb = new StringBuilder(128);
+    boolean firstModelForColour = true;
+    for (Integer model : modelAndChainRanges.keySet())
+    {
+      boolean firstPositionForModel = true;
+      if (!firstModelForColour)
       {
-        boolean firstPositionForModel = true;
-        if (!firstModelForColour)
-        {
-          sb.append("|");
-        }
-        firstModelForColour = false;
-        sb.append("#").append(model).append(":");
+        sb.append("|");
+      }
+      firstModelForColour = false;
+      sb.append("#").append(model).append(":");
 
-        final Map<String, List<int[]>> modelData = colourData.get(model);
-        for (String chain : modelData.keySet())
+      final Map<String, List<int[]>> modelData = modelAndChainRanges
+              .get(model);
+      for (String chain : modelData.keySet())
+      {
+        boolean hasChain = !"".equals(chain.trim());
+        for (int[] range : modelData.get(chain))
         {
-          boolean hasChain = !"".equals(chain.trim());
-          for (int[] range : modelData.get(chain))
+          if (!firstPositionForModel)
           {
-            if (!firstPositionForModel)
-            {
-              sb.append(",");
-            }
-            if (range[0] == range[1])
-            {
-              sb.append(range[0]);
-            }
-            else
-            {
-              sb.append(range[0]).append("-").append(range[1]);
-            }
-            if (hasChain)
-            {
-              sb.append(".").append(chain);
-            }
-            firstPositionForModel = false;
+            sb.append(",");
           }
+          if (range[0] == range[1])
+          {
+            sb.append(range[0]);
+          }
+          else
+          {
+            sb.append(range[0]).append("-").append(range[1]);
+          }
+          if (hasChain)
+          {
+            sb.append(".").append(chain);
+          }
+          firstPositionForModel = false;
         }
       }
     }
-    commands.add(sb.toString());
-    return commands;
+    return sb.toString();
   }
 
   /**
    * <pre>
-   * Build a data structure which maps contiguous subsequences for each colour. 
-   * This generates a data structure from which we can easily generate the 
-   * Chimera command for colour by sequence.
+   * Build a data structure which records contiguous subsequences for each colour. 
+   * From this we can easily generate the Chimera command for colour by sequence.
    * Color
    *     Model number
    *         Chain
@@ -162,13 +186,19 @@ public class ChimeraCommands
    * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
    * </pre>
    */
-  protected static Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> buildColoursMap(
+  protected static Map<Object, AtomSpecModel> buildColoursMap(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
-    Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
+    ColumnSelection cs = viewport.getColumnSelection();
+    AlignmentI al = viewport.getAlignment();
+    Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
     Color lastColour = null;
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -186,9 +216,9 @@ public class ChimeraCommands
         {
           final SequenceI seq = sequence[pdbfnum][s];
           if (mapping[m].getSequence() == seq
-                  && (sp = alignment.findIndex(seq)) > -1)
+                  && (sp = al.findIndex(seq)) > -1)
           {
-            SequenceI asp = alignment.getSequenceAt(sp);
+            SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
               // no mapping to gaps in sequence
@@ -203,7 +233,16 @@ public class ChimeraCommands
                 continue;
               }
 
-              Color colour = sr.getResidueColour(seq, r, fr);
+              Color colour = sr.getResidueColour(seq, r, finder);
+
+              /*
+               * darker colour for hidden regions
+               */
+              if (!cs.isVisible(r))
+              {
+                colour = Color.GRAY;
+              }
+
               final String chain = mapping[m].getChain();
 
               /*
@@ -230,8 +269,8 @@ public class ChimeraCommands
             // final colour range
             if (lastColour != null)
             {
-              addColourRange(colourMap, lastColour, pdbfnum, startPos,
-                      lastPos, lastChain);
+              addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
+                      lastChain);
             }
             // break;
           }
@@ -244,51 +283,266 @@ public class ChimeraCommands
   /**
    * Helper method to add one contiguous colour range to the colour map.
    * 
-   * @param colourMap
-   * @param colour
+   * @param map
+   * @param key
    * @param model
    * @param startPos
    * @param endPos
    * @param chain
    */
-  protected static void addColourRange(
-          Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> colourMap,
-          Color colour, int model, int startPos, int endPos, String chain)
+  protected static void addColourRange(Map<Object, AtomSpecModel> map,
+          Object key, int model, int startPos, int endPos, String chain)
   {
     /*
      * Get/initialize map of data for the colour
      */
-    SortedMap<Integer, Map<String, List<int[]>>> colourData = colourMap
-            .get(colour);
-    if (colourData == null)
+    AtomSpecModel atomSpec = map.get(key);
+    if (atomSpec == null)
     {
-      colourMap
-              .put(colour,
-                      colourData = new TreeMap<Integer, Map<String, List<int[]>>>());
+      atomSpec = new AtomSpecModel();
+      map.put(key, atomSpec);
     }
 
-    /*
-     * Get/initialize map of data for the colour and model
-     */
-    Map<String, List<int[]>> modelData = colourData.get(model);
-    if (modelData == null)
+    atomSpec.addRange(model, startPos, endPos, chain);
+  }
+
+  /**
+   * Constructs and returns Chimera commands to set attributes on residues
+   * corresponding to features in Jalview. Attribute names are the Jalview
+   * feature type, with a "jv_" prefix.
+   * 
+   * @param ssm
+   * @param files
+   * @param seqs
+   * @param viewPanel
+   * @return
+   */
+  public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
+          StructureSelectionManager ssm, String[] files,
+          SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+  {
+    Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
+            ssm, files, seqs, viewPanel);
+
+    List<String> commands = buildSetAttributeCommands(featureMap);
+
+    StructureMappingcommandSet cs = new StructureMappingcommandSet(
+            ChimeraCommands.class, null,
+            commands.toArray(new String[commands.size()]));
+
+    return cs;
+  }
+
+  /**
+   * <pre>
+   * Helper method to build a map of 
+   *   { featureType, { feature value, AtomSpecModel } }
+   * </pre>
+   * 
+   * @param ssm
+   * @param files
+   * @param seqs
+   * @param viewPanel
+   * @return
+   */
+  protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+          StructureSelectionManager ssm, String[] files,
+          SequenceI[][] seqs, AlignmentViewPanel viewPanel)
+  {
+    Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    if (fr == null)
     {
-      colourData.put(model, modelData = new TreeMap<String, List<int[]>>());
+      return theMap;
     }
 
-    /*
-     * Get/initialize map of data for colour, model and chain
-     */
-    List<int[]> chainData = modelData.get(chain);
-    if (chainData == null)
+    List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
+    if (visibleFeatures.isEmpty())
     {
-      modelData.put(chain, chainData = new ArrayList<int[]>());
+      return theMap;
     }
 
+    AlignmentI alignment = viewPanel.getAlignment();
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    {
+      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+      if (mapping == null || mapping.length < 1)
+      {
+        continue;
+      }
+
+      for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
+      {
+        for (int m = 0; m < mapping.length; m++)
+        {
+          final SequenceI seq = seqs[pdbfnum][seqNo];
+          int sp = alignment.findIndex(seq);
+          if (mapping[m].getSequence() == seq && sp > -1)
+          {
+            /*
+             * found a sequence with a mapping to a structure;
+             * now scan its features
+             */
+            SequenceI asp = alignment.getSequenceAt(sp);
+
+            scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
+                    pdbfnum);
+          }
+        }
+      }
+    }
+    return theMap;
+  }
+
+  /**
+   * Inspect features on the sequence; for each feature that is visible,
+   * determine its mapped ranges in the structure (if any) according to the
+   * given mapping, and add them to the map
+   * 
+   * @param visibleFeatures
+   * @param mapping
+   * @param seq
+   * @param theMap
+   * @param modelNumber
+   */
+  protected static void scanSequenceFeatures(List<String> visibleFeatures,
+          StructureMapping mapping, SequenceI seq,
+          Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
+  {
+    SequenceFeature[] sfs = seq.getSequenceFeatures();
+    if (sfs == null)
+    {
+      return;
+    }
+
+    for (SequenceFeature sf : sfs)
+    {
+      String type = sf.getType();
+
+      /*
+       * Only copy visible features, don't copy any which originated
+       * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
+       */
+      boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+              .equals(sf.getFeatureGroup());
+      if (isFromViewer || !visibleFeatures.contains(type))
+      {
+        continue;
+      }
+      List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
+              sf.getEnd());
+
+      if (!mappedRanges.isEmpty())
+      {
+        String value = sf.getDescription();
+        if (value == null || value.length() == 0)
+        {
+          value = type;
+        }
+        float score = sf.getScore();
+        if (score != 0f && !Float.isNaN(score))
+        {
+          value = Float.toString(score);
+        }
+        Map<Object, AtomSpecModel> featureValues = theMap.get(type);
+        if (featureValues == null)
+        {
+          featureValues = new HashMap<Object, AtomSpecModel>();
+          theMap.put(type, featureValues);
+        }
+        for (int[] range : mappedRanges)
+        {
+          addColourRange(featureValues, value, modelNumber, range[0], range[1],
+                  mapping.getChain());
+        }
+      }
+    }
+  }
+
+  /**
+   * Traverse the map of features/values/models/chains/positions to construct a
+   * list of 'setattr' commands (one per distinct feature type and value).
+   * <p>
+   * The format of each command is
+   * 
+   * <pre>
+   * <blockquote> setattr r <featureName> " " #modelnumber:range.chain 
+   * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+   * </blockquote>
+   * </pre>
+   * 
+   * @param featureMap
+   * @return
+   */
+  protected static List<String> buildSetAttributeCommands(
+          Map<String, Map<Object, AtomSpecModel>> featureMap)
+  {
+    List<String> commands = new ArrayList<String>();
+    for (String featureType : featureMap.keySet())
+    {
+      String attributeName = makeAttributeName(featureType);
+
+      /*
+       * clear down existing attributes for this feature
+       */
+      // 'problem' - sets attribute to None on all residues - overkill?
+      // commands.add("~setattr r " + attributeName + " :*");
+
+      Map<Object, AtomSpecModel> values = featureMap.get(featureType);
+      for (Object value : values.keySet())
+      {
+        /*
+         * for each distinct value recorded for this feature type,
+         * add a command to set the attribute on the mapped residues
+         * Put values in single quotes, encoding any embedded single quotes
+         */
+        StringBuilder sb = new StringBuilder(128);
+        String featureValue = value.toString();
+        featureValue = featureValue.replaceAll("\\'", "&#39;");
+        sb.append("setattr r ").append(attributeName).append(" '")
+                .append(featureValue).append("' ");
+        sb.append(values.get(value).getAtomSpec());
+        commands.add(sb.toString());
+      }
+    }
+
+    return commands;
+  }
+
+  /**
+   * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
+   * for a 'Jalview' namespace, and any non-alphanumeric character is converted
+   * to an underscore.
+   * 
+   * @param featureType
+   * @return <pre>
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   * </pre>
+   */
+  protected static String makeAttributeName(String featureType)
+  {
+    StringBuilder sb = new StringBuilder();
+    if (featureType != null)
+    {
+      for (char c : featureType.toCharArray())
+      {
+        sb.append(Character.isLetterOrDigit(c) ? c : '_');
+      }
+    }
+    String attName = NAMESPACE_PREFIX + sb.toString();
+
     /*
-     * Add the start/end positions
+     * Chimera treats an attribute name ending in 'color' as colour-valued;
+     * Jalview doesn't, so prevent this by appending an underscore
      */
-    chainData.add(new int[] { startPos, endPos });
+    if (attName.toUpperCase().endsWith("COLOR"))
+    {
+      attName += "_";
+    }
+
+    return attName;
   }
 
 }
diff --git a/src/jalview/ext/rbvi/chimera/ChimeraListener.java b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
index ba5e332..507ddbc 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraListener.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraListener.java
@@ -129,7 +129,7 @@ public class ChimeraListener extends AbstractRequestHandler implements
   }
 
   /**
-   * Handler a ModelChanged notification from Chimera
+   * Handle a ModelChanged notification from Chimera
    * 
    * @param substring
    */
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index b05c168..fad3137 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -21,13 +21,15 @@
 package jalview.ext.rbvi.chimera;
 
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.httpserver.AbstractRequestHandler;
 import jalview.io.DataSourceType;
@@ -40,8 +42,14 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.net.BindException;
 import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Collections;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -54,6 +62,8 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
 
 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 {
+  public static final String CHIMERA_FEATURE_GROUP = "Chimera";
+
   // Chimera clause to exclude alternate locations in atom selection
   private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
 
@@ -98,14 +108,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
 
-  /*
-   * the default or current model displayed if the model cannot be identified
-   * from the selection message
-   */
-  private int frameNo = 0;
-
-  private String lastCommand;
-
   String lastHighlightCommand;
 
   /*
@@ -171,11 +173,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       {
         getSsm().addStructureViewerListener(this);
         // ssm.addSelectionListener(this);
-        FeatureRenderer fr = getFeatureRenderer(null);
-        if (fr != null)
-        {
-          fr.featuresAdded();
-        }
         refreshGUI();
       }
       return true;
@@ -304,7 +301,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       chimeraListener.shutdown();
       chimeraListener = null;
     }
-    lastCommand = null;
     viewer = null;
 
     if (chimeraMonitor != null)
@@ -339,21 +335,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Construct and send a command to align structures against a reference
-   * structure, based on one or more sequence alignments
-   * 
-   * @param _alignment
-   *          an array of alignments to process
-   * @param _refStructure
-   *          an array of corresponding reference structures (index into pdb
-   *          file array); if a negative value is passed, the first PDB file
-   *          mapped to an alignment sequence is used as the reference for
-   *          superposition
-   * @param _hiddenCols
-   *          an array of corresponding hidden columns for each alignment
+   * {@inheritDoc}
    */
   @Override
-  public void superposeStructures(AlignmentI[] _alignment,
+  public String superposeStructures(AlignmentI[] _alignment,
           int[] _refStructure, ColumnSelection[] _hiddenCols)
   {
     StringBuilder allComs = new StringBuilder(128);
@@ -361,7 +346,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
     if (!waitForFileLoad(files))
     {
-      return;
+      return null;
     }
 
     refreshPdbEntries();
@@ -380,13 +365,16 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       }
 
       /*
-       * 'matched' array will hold 'true' for visible alignment columns where
+       * 'matched' bit i will be set for visible alignment columns i where
        * all sequences have a residue with a mapping to the PDB structure
        */
-      boolean matched[] = new boolean[alignment.getWidth()];
-      for (int m = 0; m < matched.length; m++)
+      BitSet matched = new BitSet();
+      for (int m = 0; m < alignment.getWidth(); m++)
       {
-        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+        if (hiddenCols == null || hiddenCols.isVisible(m))
+        {
+          matched.set(m);
+        }
       }
 
       SuperposeData[] structures = new SuperposeData[files.length];
@@ -410,17 +398,11 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
         refStructure = candidateRefStructure;
       }
 
-      int nmatched = 0;
-      for (boolean b : matched)
-      {
-        if (b)
-        {
-          nmatched++;
-        }
-      }
+      int nmatched = matched.cardinality();
       if (nmatched < 4)
       {
-        // TODO: bail out here because superposition illdefined?
+        return MessageManager.formatMessage("label.insufficient_residues",
+                nmatched);
       }
 
       /*
@@ -433,41 +415,41 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
         int lpos = -1;
         boolean run = false;
         StringBuilder molsel = new StringBuilder();
-        for (int r = 0; r < matched.length; r++)
+
+        int nextColumnMatch = matched.nextSetBit(0);
+        while (nextColumnMatch != -1)
         {
-          if (matched[r])
+          int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
+          if (lpos != pdbResNum - 1)
           {
-            int pdbResNum = structures[pdbfnum].pdbResNo[r];
-            if (lpos != pdbResNum - 1)
+            /*
+             * discontiguous - append last residue now
+             */
+            if (lpos != -1)
             {
-              /*
-               * discontiguous - append last residue now
-               */
-              if (lpos != -1)
-              {
-                molsel.append(String.valueOf(lpos));
-                molsel.append(chainCd);
-                molsel.append(",");
-              }
-              run = false;
+              molsel.append(String.valueOf(lpos));
+              molsel.append(chainCd);
+              molsel.append(",");
             }
-            else
+            run = false;
+          }
+          else
+          {
+            /*
+             * extending a contiguous run
+             */
+            if (!run)
             {
               /*
-               * extending a contiguous run
+               * start the range selection
                */
-              if (!run)
-              {
-                /*
-                 * start the range selection
-                 */
-                molsel.append(String.valueOf(lpos));
-                molsel.append("-");
-              }
-              run = true;
+              molsel.append(String.valueOf(lpos));
+              molsel.append("-");
             }
-            lpos = pdbResNum;
+            run = true;
           }
+          lpos = pdbResNum;
+          nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
         }
 
         /*
@@ -543,6 +525,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
                 .append(";" + command.toString());
       }
     }
+
+    String error = null;
     if (selectioncom.length() > 0)
     {
       // TODO: visually distinguish regions that were superposed
@@ -556,9 +540,17 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       }
       allComs.append("; ~display all; chain @CA|P; ribbon ")
               .append(selectioncom.toString()).append("; focus");
-      sendChimeraCommand(allComs.toString(), false);
+      List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
+              true);
+      for (String reply : chimeraReplies)
+      {
+        if (reply.toLowerCase().contains("unequal numbers of atoms"))
+        {
+          error = reply;
+        }
+      }
     }
-
+    return error;
   }
 
   /**
@@ -631,31 +623,42 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Send a command to Chimera, and optionally log any responses.
+   * Send a command to Chimera, and optionally log and return any responses.
+   * <p>
+   * Does nothing, and returns null, if the command is the same as the last one
+   * sent [why?].
    * 
    * @param command
-   * @param logResponse
+   * @param getResponse
    */
-  public void sendChimeraCommand(final String command, boolean logResponse)
+  public List<String> sendChimeraCommand(final String command,
+          boolean getResponse)
   {
     if (viewer == null)
     {
       // ? thread running after viewer shut down
-      return;
+      return null;
     }
+    List<String> reply = null;
     viewerCommandHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command))
+    if (true /*lastCommand == null || !lastCommand.equals(command)*/)
     {
       // trim command or it may never find a match in the replyLog!!
       List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
-              logResponse);
-      if (logResponse && debug)
+              getResponse);
+      if (getResponse)
       {
-        log("Response from command ('" + command + "') was:\n" + lastReply);
+        reply = lastReply;
+        if (debug)
+        {
+          log("Response from command ('" + command + "') was:\n"
+                  + lastReply);
+        }
       }
     }
     viewerCommandHistory(true);
-    lastCommand = command;
+
+    return reply;
   }
 
   /**
@@ -689,17 +692,15 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /**
    * @param files
    * @param sr
-   * @param fr
-   * @param alignment
+   * @param viewPanel
    * @return
    */
   @Override
   protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+          String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
   {
     return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, alignment);
+            getSequence(), sr, viewPanel);
   }
 
   /**
@@ -742,6 +743,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
+
   // ////////////////////////////////
   // /StructureListener
   @Override
@@ -837,59 +839,64 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * Parse model number, residue and chain for each selected position,
      * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
      */
+    List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
+
+    /*
+     * Broadcast the selection (which may be empty, if the user just cleared all
+     * selections)
+     */
+    getSsm().mouseOverStructure(atomSpecs);
+  }
+
+  /**
+   * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
+   * corresponding residues (if any) in Jalview
+   * 
+   * @param structureSelection
+   * @return
+   */
+  protected List<AtomSpec> convertStructureResiduesToAlignment(
+          List<String> structureSelection)
+  {
     List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
-    for (String atomSpec : selection)
+    for (String atomSpec : structureSelection)
     {
-      int colonPos = atomSpec.indexOf(":");
-      if (colonPos == -1)
-      {
-        continue; // malformed
-      }
-
-      int hashPos = atomSpec.indexOf("#");
-      String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
-      int dotPos = modelSubmodel.indexOf(".");
-      int modelId = 0;
       try
       {
-        modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
-                : modelSubmodel.substring(0, dotPos));
-      } catch (NumberFormatException e)
+        AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
+        String pdbfilename = getPdbFileForModel(spec.getModelNumber());
+        spec.setPdbFile(pdbfilename);
+        atomSpecs.add(spec);
+      } catch (IllegalArgumentException e)
       {
-        // ignore, default to model 0
+        System.err.println("Failed to parse atomspec: " + atomSpec);
       }
+    }
+    return atomSpecs;
+  }
 
-      String residueChain = atomSpec.substring(colonPos + 1);
-      dotPos = residueChain.indexOf(".");
-      int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
-              : residueChain.substring(0, dotPos));
-
-      String chainId = dotPos == -1 ? "" : residueChain
-              .substring(dotPos + 1);
-
-      /*
-       * Work out the pdbfilename from the model number
-       */
-      String pdbfilename = modelFileNames[frameNo];
-      findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
+  /**
+   * @param modelId
+   * @return
+   */
+  protected String getPdbFileForModel(int modelId)
+  {
+    /*
+     * Work out the pdbfilename from the model number
+     */
+    String pdbfilename = modelFileNames[0];
+    findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
+    {
+      for (ChimeraModel cm : chimeraMaps.get(pdbfile))
       {
-        for (ChimeraModel cm : chimeraMaps.get(pdbfile))
+        if (cm.getModelNumber() == modelId)
         {
-          if (cm.getModelNumber() == modelId)
-          {
-            pdbfilename = pdbfile;
-            break findfileloop;
-          }
+          pdbfilename = pdbfile;
+          break findfileloop;
         }
       }
-      atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
     }
-
-    /*
-     * Broadcast the selection (which may be empty, if the user just cleared all
-     * selections)
-     */
-    getSsm().mouseOverStructure(atomSpecs);
+    return pdbfilename;
   }
 
   private void log(String message)
@@ -1036,6 +1043,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
+   * Returns a list of chains mapped in this viewer. Note this list is not
+   * currently scoped per structure.
+   * 
+   * @return
+   */
+  @Override
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
+
+  /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
   public void focusView()
@@ -1071,13 +1090,207 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
   }
 
+  /**
+   * Constructs and send commands to Chimera to set attributes on residues for
+   * features visible in Jalview
+   * 
+   * @param avp
+   * @return
+   */
+  public int sendFeaturesToViewer(AlignmentViewPanel avp)
+  {
+    // TODO refactor as required to pull up to an interface
+    AlignmentI alignment = avp.getAlignment();
 
-  @Override
-  public List<String> getChainNames()
+    String[] files = getPdbFile();
+    if (files == null)
+    {
+      return 0;
+    }
+
+    StructureMappingcommandSet commandSet = ChimeraCommands
+            .getSetAttributeCommandsForFeatures(getSsm(), files,
+                    getSequence(), avp);
+    String[] commands = commandSet.commands;
+    if (commands.length > 10)
+    {
+      sendCommandsByFile(commands);
+    }
+    else
+    {
+      for (String command : commands)
+      {
+        sendAsynchronousCommand(command, null);
+      }
+    }
+    return commands.length;
+  }
+
+  /**
+   * Write commands to a temporary file, and send a command to Chimera to open
+   * the file as a commands script. For use when sending a large number of
+   * separate commands would overload the REST interface mechanism.
+   * 
+   * @param commands
+   */
+  protected void sendCommandsByFile(String[] commands)
   {
-    return chainNames;
+    try
+    {
+      File tmp = File.createTempFile("chim", ".com");
+      tmp.deleteOnExit();
+      PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
+      for (String command : commands)
+      {
+        out.println(command);
+      }
+      out.flush();
+      out.close();
+      String path = tmp.getAbsolutePath();
+      sendAsynchronousCommand("open cmd:" + path, null);
+    } catch (IOException e)
+    {
+      System.err
+              .println("Sending commands to Chimera via file failed with "
+                      + e.getMessage());
+    }
   }
 
+  /**
+   * Get Chimera residues which have the named attribute, find the mapped
+   * positions in the Jalview sequence(s), and set as sequence features
+   * 
+   * @param attName
+   * @param alignmentPanel
+   */
+  public void copyStructureAttributesToFeatures(String attName,
+          AlignmentViewPanel alignmentPanel)
+  {
+    // todo pull up to AAStructureBindingModel (and interface?)
+
+    /*
+     * ask Chimera to list residues with the attribute, reporting its value
+     */
+    // this alternative command
+    // list residues spec ':*/attName' attr attName
+    // doesn't report 'None' values (which is good), but
+    // fails for 'average.bfactor' (which is bad):
+
+    String cmd = "list residues attr '" + attName + "'";
+    List<String> residues = sendChimeraCommand(cmd, true);
+
+    boolean featureAdded = createFeaturesForAttributes(attName, residues);
+    if (featureAdded)
+    {
+      alignmentPanel.getFeatureRenderer().featuresAdded();
+    }
+  }
+
+  /**
+   * Create features in Jalview for the given attribute name and structure
+   * residues.
+   * 
+   * <pre>
+   * The residue list should be 0, 1 or more reply lines of the format: 
+   *     residue id #0:5.A isHelix -155.000836316 index 5 
+   * or 
+   *     residue id #0:6.A isHelix None
+   * </pre>
+   * 
+   * @param attName
+   * @param residues
+   * @return
+   */
+  protected boolean createFeaturesForAttributes(String attName,
+          List<String> residues)
+  {
+    boolean featureAdded = false;
+    String featureGroup = getViewerFeatureGroup();
+
+    for (String residue : residues)
+    {
+      AtomSpec spec = null;
+      String[] tokens = residue.split(" ");
+      if (tokens.length < 5)
+      {
+        continue;
+      }
+      String atomSpec = tokens[2];
+      String attValue = tokens[4];
+
+      /*
+       * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
+       */
+      if ("None".equalsIgnoreCase(attValue)
+              || "False".equalsIgnoreCase(attValue))
+      {
+        continue;
+      }
+
+      try
+      {
+        spec = AtomSpec.fromChimeraAtomspec(atomSpec);
+      } catch (IllegalArgumentException e)
+      {
+        System.err.println("Problem parsing atomspec " + atomSpec);
+        continue;
+      }
+
+      String chainId = spec.getChain();
+      String description = attValue;
+      float score = Float.NaN;
+      try
+      {
+        score = Float.valueOf(attValue);
+        description = chainId;
+      } catch (NumberFormatException e)
+      {
+        // was not a float value
+      }
+
+      String pdbFile = getPdbFileForModel(spec.getModelNumber());
+      spec.setPdbFile(pdbFile);
+
+      List<AtomSpec> atoms = Collections.singletonList(spec);
+
+      /*
+       * locate the mapped position in the alignment (if any)
+       */
+      SearchResultsI sr = getSsm()
+              .findAlignmentPositionsForStructurePositions(atoms);
+
+      /*
+       * expect one matched alignment position, or none 
+       * (if the structure position is not mapped)
+       */
+      for (SearchResultMatchI m : sr.getResults())
+      {
+        SequenceI seq = m.getSequence();
+        int start = m.getStart();
+        int end = m.getEnd();
+        SequenceFeature sf = new SequenceFeature(attName, description,
+                start, end, score, featureGroup);
+        // todo: should SequenceFeature have an explicit property for chain?
+        // note: repeating the action shouldn't duplicate features
+        featureAdded |= seq.addSequenceFeature(sf);
+      }
+    }
+    return featureAdded;
+  }
+
+  /**
+   * Answers the feature group name to apply to features created in Jalview from
+   * Chimera attributes
+   * 
+   * @return
+   */
+  protected String getViewerFeatureGroup()
+  {
+    // todo pull up to interface
+    return CHIMERA_FEATURE_GROUP;
+  }
+
+
   public Hashtable<String, String> getChainFile()
   {
     return chainFile;
diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index a41e10e..d65f1d5 100644
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -20,10 +20,10 @@
  */
 package jalview.ext.varna;
 
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
 
@@ -47,7 +47,8 @@ public class VarnaCommands
    */
   public static String[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+          SequenceI[][] sequence, SequenceRenderer sr,
+          FeatureColourFinder finder,
           AlignmentI alignment)
   {
     ArrayList<String> str = new ArrayList<String>();
@@ -58,7 +59,9 @@ public class VarnaCommands
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
 
       if (mapping == null || mapping.length < 1)
+      {
         continue;
+      }
 
       int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
@@ -79,14 +82,15 @@ public class VarnaCommands
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
               if (pos < 1 || pos == lastPos)
+              {
                 continue;
+              }
 
               lastPos = pos;
 
-              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+              Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+                      finder);
 
-              if (fr != null)
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                       + "/"
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c7bce10..507bfab 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -86,6 +86,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.jws1.Discoverer;
@@ -160,6 +161,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   AlignViewport viewport;
 
+  ViewportRanges vpRanges;
+
   public AlignViewControllerI avc;
 
   List<AlignmentPanel> alignPanels = new ArrayList<AlignmentPanel>();
@@ -331,6 +334,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
+    vpRanges = viewport.getRanges();
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
@@ -640,8 +644,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   new String[] { (viewport.cursorMode ? "on" : "off") }));
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().seqCanvas.cursorX = viewport.startRes;
-            alignPanel.getSeqPanel().seqCanvas.cursorY = viewport.startSeq;
+            alignPanel.getSeqPanel().seqCanvas.cursorX = vpRanges
+                    .getStartRes();
+            alignPanel.getSeqPanel().seqCanvas.cursorY = vpRanges
+                    .getStartSeq();
           }
           alignPanel.getSeqPanel().seqCanvas.repaint();
           break;
@@ -679,8 +685,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                    - viewport.endSeq + viewport.startSeq);
+            alignPanel.setScrollValues(vpRanges.getStartRes(),
+                    2 * vpRanges.getStartSeq() - vpRanges.getEndSeq());
           }
           break;
         case KeyEvent.VK_PAGE_DOWN:
@@ -690,8 +696,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
-                    + viewport.endSeq - viewport.startSeq);
+            alignPanel.setScrollValues(vpRanges.getStartRes(),
+                    vpRanges.getEndSeq());
           }
           break;
         }
@@ -2141,7 +2147,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        viewport.setEndSeq(alignment.getHeight());
+        vpRanges.setEndSeq(alignment.getHeight());
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -2545,7 +2551,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
                 column, viewport.getAlignment());
-        viewport.setStartRes(0);
+        vpRanges.setStartRes(0);
       }
       else
       {
@@ -2612,13 +2618,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(vpRanges.getStartRes());
     // ShiftList shifts;
     // viewport.getAlignment().removeGaps(shifts=new ShiftList());
     // edit.alColumnChanges=shifts.getInverse();
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
 
@@ -2651,12 +2657,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // This is to maintain viewport position on first residue
     // of first sequence
     SequenceI seq = viewport.getAlignment().getSequenceAt(0);
-    int startRes = seq.findPosition(viewport.startRes);
+    int startRes = seq.findPosition(vpRanges.getStartRes());
 
     addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
             viewport.getAlignment()));
 
-    viewport.setStartRes(seq.findIndex(startRes) - 1);
+    vpRanges.setStartRes(seq.findIndex(startRes) - 1);
 
     viewport.firePropertyChange("alignment", null, viewport.getAlignment()
             .getSequences());
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index e0efa7c..602e3a1 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -46,12 +46,12 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Container;
@@ -72,7 +72,7 @@ import javax.swing.JInternalFrame;
  * @version $Revision: 1.141 $
  */
 public class AlignViewport extends AlignmentViewport implements
-        SelectionSource, CommandListener
+        SelectionSource
 {
   Font font;
 
@@ -238,10 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   void init()
   {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
+    ranges = new ViewportRanges(this.alignment);
     applyViewProperties();
 
     String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -855,7 +852,7 @@ public class AlignViewport extends AlignmentViewport implements
       }
     }
 
-    setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f7a1d2c..8ade5d6 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -35,6 +35,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -69,6 +70,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 {
   public AlignViewport av;
 
+  ViewportRanges vpRanges;
+
   OverviewPanel overviewPanel;
 
   private SeqPanel seqPanel;
@@ -91,9 +94,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  int hextent = 0;
+  private int hextent = 0;
 
-  int vextent = 0;
+  private int vextent = 0;
 
   /*
    * Flag set while scrolling to follow complementary cDNA/protein scroll. When
@@ -113,6 +116,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     alignFrame = af;
     this.av = av;
+    vpRanges = av.getRanges();
     setSeqPanel(new SeqPanel(av, this));
     setIdPanel(new IdPanel(av, this));
 
@@ -377,7 +381,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       if (centre)
       {
-        int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+        int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
         end = end + offset - 1;
       }
@@ -413,7 +417,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
-        if ((startv = av.getStartRes()) >= start)
+        if ((startv = vpRanges.getStartRes()) >= start)
         {
           /*
            * Scroll left to make start of search results visible
@@ -421,7 +425,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(start - 1, seqIndex); // plus one residue
           setScrollValues(start, seqIndex);
         }
-        else if ((endv = av.getEndRes()) <= end)
+        else if ((endv = vpRanges.getEndRes()) <= end)
         {
           /*
            * Scroll right to make end of search results visible
@@ -429,19 +433,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
           setScrollValues(startv + end - endv, seqIndex);
         }
-        else if ((starts = av.getStartSeq()) > seqIndex)
+        else if ((starts = vpRanges.getStartSeq()) > seqIndex)
         {
           /*
            * Scroll up to make start of search results visible
            */
-          setScrollValues(av.getStartRes(), seqIndex);
+          setScrollValues(vpRanges.getStartRes(), seqIndex);
         }
-        else if ((ends = av.getEndSeq()) <= seqIndex)
+        else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
         {
           /*
            * Scroll down to make end of search results visible
            */
-          setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+          setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+                  + 1);
         }
         /*
          * Else results are already visible - no need to scroll
@@ -464,10 +469,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
   {
     int cwidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-    if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
+    if (res < vpRanges.getStartRes()
+            || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
-      av.startRes = vscroll.getValue() * cwidth;
+      vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
 
   }
@@ -591,7 +597,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    av.startSeq = 0;
+    vpRanges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -688,7 +694,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;
@@ -698,12 +703,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.hasHiddenColumns())
     {
+      // reset the width to exclude hidden columns
       width = av.getColumnSelection().findColumnPosition(width);
     }
 
-    av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
-            .getCharWidth())) - 1);
-
     hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
     vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -737,6 +740,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       x = 0;
     }
 
+    // update endRes after x has (possibly) been adjusted
+    vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+            .getCharWidth())) - 1);
+
     /*
      * each scroll adjustment triggers adjustmentValueChanged, which resets the
      * 'do not scroll complement' flag; ensure it is the same for both
@@ -757,14 +764,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
-    int oldX = av.getStartRes();
-    int oldY = av.getStartSeq();
+    int oldX = vpRanges.getStartRes();
+    int oldY = vpRanges.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
-      av.setStartRes(x);
-      av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+      vpRanges.setStartRes(x);
+      vpRanges.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
               .getCharWidth())) - 1);
     }
 
@@ -778,8 +785,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         {
           int rowSize = getSeqPanel().seqCanvas
                   .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
-          av.setStartRes(offy * rowSize);
-          av.setEndRes((offy + 1) * rowSize);
+          vpRanges.setStartRes(offy * rowSize);
+          vpRanges.setEndRes((offy + 1) * rowSize);
         }
         else
         {
@@ -791,16 +798,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
             @Override
             public void run()
             {
-              setScrollValues(av.getStartRes(), av.getStartSeq());
+              setScrollValues(vpRanges.getStartRes(),
+                      vpRanges.getStartSeq());
             }
           });
         }
       }
       else
       {
-        av.setStartSeq(offy);
-        av.setEndSeq(offy
-                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
+        vpRanges.setStartSeq(offy);
+        vpRanges.setEndSeq(offy
+                + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())
+                - 1);
       }
     }
 
@@ -809,8 +818,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       overviewPanel.setBoxPosition();
     }
 
-    int scrollX = av.startRes - oldX;
-    int scrollY = av.startSeq - oldY;
+    int scrollX = vpRanges.getStartRes() - oldX;
+    int scrollY = vpRanges.getStartSeq() - oldY;
 
     if (av.getWrapAlignment() || !fastPaint)
     {
@@ -820,13 +829,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       // Make sure we're not trying to draw a panel
       // larger than the visible window
-      if (scrollX > av.endRes - av.startRes)
+      if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
       {
-        scrollX = av.endRes - av.startRes;
+        scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
       }
-      else if (scrollX < av.startRes - av.endRes)
+      else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
       {
-        scrollX = av.startRes - av.endRes;
+        scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
       }
 
       if (scrollX != 0 || scrollY != 0)
@@ -926,7 +935,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      setScrollValues(av.getStartRes(), av.getStartSeq());
+      setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
     }
   }
 
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index f6352d7..8500888 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -21,6 +21,8 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -35,9 +37,11 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Hashtable;
+import java.util.Vector;
 
 import javax.swing.BorderFactory;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JColorChooser;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
@@ -49,27 +53,21 @@ import net.miginfocom.swing.MigLayout;
 @SuppressWarnings("serial")
 public class AnnotationColourChooser extends AnnotationRowFilter
 {
+  private static final int ONETHOUSAND = 1000;
 
-  ColourSchemeI oldcs;
+  private ColourSchemeI oldcs;
 
-  Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
+  private JButton defColours;
 
-  /**
-   * enabled if the user is dragging the slider - try to keep updates to a
-   * minimun
-   */
+  private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  JComboBox<String> annotations;
+  private JCheckBox useOriginalColours = new JCheckBox();
 
-  JButton defColours = new JButton();
+  private JPanel minColour = new JPanel();
 
-  JPanel jPanel1 = new JPanel();
+  private JPanel maxColour = new JPanel();
 
-  JPanel jPanel2 = new JPanel();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  private JComboBox<String> threshold = new JComboBox<String>();
+  private JCheckBox thresholdIsMin = new JCheckBox();
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
@@ -108,7 +106,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.isPredefinedColours()
+      useOriginalColours.setSelected(acg.isPredefinedColours()
               || acg.getBaseColour() != null);
       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
       {
@@ -118,15 +116,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       seqAssociated.setSelected(acg.isSeqAssociated());
 
     }
-    annotations = new JComboBox<String>(
-            getAnnotationItems(seqAssociated.isSelected()));
+    Vector<String> annotItems = getAnnotationItems(seqAssociated
+            .isSelected());
+    annotations = new JComboBox<String>(annotItems);
 
     populateThresholdComboBox(threshold);
 
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.setSelectedItem(acg.getAnnotation());
+      String label = getAnnotationMenuLabel(acg.getAnnotation());
+      annotations.setSelectedItem(label);
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
@@ -143,16 +143,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 MessageManager
                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
       }
-      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
       thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-    }
+    jbInit();
     adjusting = false;
 
     updateView();
@@ -160,19 +155,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     frame.pack();
   }
 
-  public AnnotationColourChooser()
+  @Override
+  protected void jbInit()
   {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
+    super.jbInit();
 
-  private void jbInit() throws Exception
-  {
     minColour.setFont(JvSwingUtils.getLabelFont());
     minColour.setBorder(BorderFactory.createEtchedBorder());
     minColour.setPreferredSize(new Dimension(40, 20));
@@ -203,26 +190,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         }
       }
     });
-    ok.setOpaque(false);
-    ok.setText(MessageManager.getString("action.ok"));
-    ok.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed();
-      }
-    });
-    cancel.setOpaque(false);
-    cancel.setText(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed();
-      }
-    });
+
+    defColours = new JButton();
     defColours.setOpaque(false);
     defColours.setText(MessageManager.getString("action.set_defaults"));
     defColours.setToolTipText(MessageManager
@@ -237,48 +206,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       }
     });
 
-    annotations.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed();
-      }
-    });
-    getThreshold().addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed();
-      }
-    });
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed();
-      }
-    });
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    currentColours.setFont(JvSwingUtils.getLabelFont());
-    currentColours.setOpaque(false);
-    currentColours.setText(MessageManager
+    useOriginalColours.setFont(JvSwingUtils.getLabelFont());
+    useOriginalColours.setOpaque(false);
+    useOriginalColours.setText(MessageManager
             .getString("label.use_original_colours"));
-    currentColours.addActionListener(new ActionListener()
+    useOriginalColours.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        currentColours_actionPerformed();
+        originalColours_actionPerformed();
       }
     });
     thresholdIsMin.setBackground(Color.white);
@@ -307,7 +244,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       }
     });
 
-    this.setLayout(borderLayout1);
+    this.setLayout(new BorderLayout());
+    JPanel jPanel1 = new JPanel();
+    JPanel jPanel2 = new JPanel();
     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
     jPanel1.setBackground(Color.white);
     jPanel2.setBackground(Color.white);
@@ -316,7 +255,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     jPanel1.add(cancel);
     jPanel2.add(annotations, "grow, wrap");
     jPanel2.add(seqAssociated);
-    jPanel2.add(currentColours);
+    jPanel2.add(useOriginalColours);
     JPanel colpanel = new JPanel(new FlowLayout());
     colpanel.setBackground(Color.white);
     colpanel.add(minColour);
@@ -391,7 +330,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   {
     if (slider.isEnabled())
     {
-      if (currentColours.isSelected()
+      if (useOriginalColours.isSelected()
               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
         updateView();
@@ -403,24 +342,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     }
   }
 
-  public JComboBox<String> getThreshold()
+  public void originalColours_actionPerformed()
   {
-    return threshold;
-  }
-
-  public void setThreshold(JComboBox<String> threshold)
-  {
-    this.threshold = threshold;
-  }
-
-  public void currentColours_actionPerformed()
-  {
-    if (currentColours.isSelected())
+    boolean selected = useOriginalColours.isSelected();
+    if (selected)
     {
       reset();
     }
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
+    maxColour.setEnabled(!selected);
+    minColour.setEnabled(!selected);
+    thresholdIsMin.setEnabled(!selected);
     updateView();
   }
 
@@ -441,7 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
-    thresholdIsMin.setEnabled(true);
+    thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
@@ -455,7 +386,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     {
       getCurrentAnnotation()
               .setThreshold(
-                      new jalview.datamodel.GraphLine(
+                      new GraphLine(
                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
                               "Threshold", Color.black));
     }
@@ -463,19 +394,19 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      float range = getCurrentAnnotation().graphMax * ONETHOUSAND
+              - getCurrentAnnotation().graphMin * ONETHOUSAND;
 
-      slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
-      slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
-      slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+      slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
+      slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
+      slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
       slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 
     ap.alignmentChanged();
     // ensure all associated views (overviews, structures, etc) are notified of
@@ -483,4 +414,60 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     ap.paintAlignment(true);
   }
 
+  protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
+  {
+  
+    AnnotationColourGradient acg = null;
+    if (useOriginalColours.isSelected())
+    {
+      acg = new AnnotationColourGradient(currentAnn,
+              av.getGlobalColourScheme(), selectedThresholdOption);
+    }
+    else
+    {
+      acg = new AnnotationColourGradient(currentAnn,
+              minColour.getBackground(), maxColour.getBackground(),
+              selectedThresholdOption);
+    }
+    acg.setSeqAssociated(seqAssociated.isSelected());
+  
+    if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+    {
+      acg.setPredefinedColours(true);
+    }
+  
+    acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+  
+    av.setGlobalColourScheme(acg);
+  
+    if (av.getAlignment().getGroups() != null)
+    {
+  
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        if (sg.cs == null)
+        {
+          continue;
+        }
+  
+        if (useOriginalColours.isSelected())
+        {
+          sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
+                  .getColourScheme(), selectedThresholdOption));
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+        }
+        else
+        {
+          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
+                  minColour.getBackground(), maxColour.getBackground(),
+                  selectedThresholdOption));
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+        }
+      }
+    }
+    return false;
+  }
+
 }
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 1290d70..637eb30 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -30,7 +30,6 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
 import java.awt.Color;
-import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
@@ -55,28 +54,10 @@ import net.miginfocom.swing.MigLayout;
 public class AnnotationColumnChooser extends AnnotationRowFilter implements
         ItemListener
 {
-
-  private JComboBox<String> annotations;
-
-  private JPanel actionPanel = new JPanel();
-
-  private JPanel thresholdPanel = new JPanel();
-
   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
 
-  private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
-          .getLayout());
-
-  private JPanel noGraphFilterView = new JPanel();
-
-  private JPanel graphFilterView = new JPanel();
-
   private JPanel annotationComboBoxPanel = new JPanel();
 
-  private BorderLayout borderLayout1 = new BorderLayout();
-
-  private JComboBox<String> threshold = new JComboBox<String>();
-
   private StructureFilterPanel gStructureFilterPanel;
 
   private StructureFilterPanel ngStructureFilterPanel;
@@ -107,17 +88,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private ColumnSelection oldColumnSelection;
 
-  public AnnotationColumnChooser()
-  {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
   {
     super(av, ap);
@@ -169,72 +139,27 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     frame.pack();
   }
 
-  private void jbInit() throws Exception
+  @Override
+  protected void jbInit()
   {
-    ok.setOpaque(false);
-    ok.setText(MessageManager.getString("action.ok"));
-    ok.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed();
-      }
-    });
-
-    cancel.setOpaque(false);
-    cancel.setText(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed();
-      }
-    });
-
-    annotations.addItemListener(this);
-    annotations.setToolTipText(MessageManager
-            .getString("info.select_annotation_row"));
-    threshold.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed();
-      }
-    });
-
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed();
-      }
-    });
-
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
+    super.jbInit();
 
+    JPanel thresholdPanel = new JPanel();
     thresholdPanel.setBorder(new TitledBorder(MessageManager
             .getString("label.threshold_filter")));
     thresholdPanel.setBackground(Color.white);
     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 
+    JPanel actionPanel = new JPanel();
     actionPanel.setBackground(Color.white);
     actionPanel.setFont(JvSwingUtils.getLabelFont());
 
+    JPanel graphFilterView = new JPanel();
     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     graphFilterView.setBackground(Color.white);
 
+    JPanel noGraphFilterView = new JPanel();
     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     noGraphFilterView.setBackground(Color.white);
 
@@ -270,7 +195,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     switchableViewsPanel.add(graphFilterView,
             AnnotationColumnChooser.GRAPH_VIEW);
 
-    this.setLayout(borderLayout1);
+    this.setLayout(new BorderLayout());
     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
@@ -280,7 +205,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     this.validate();
   }
 
-  public void updateThresholdPanelToolTip()
+  protected void updateThresholdPanelToolTip()
   {
     thresholdValue.setToolTipText("");
     slider.setToolTipText("");
@@ -297,7 +222,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   }
 
   @Override
-  public void reset()
+  protected void reset()
   {
     if (this.getOldColumnSelection() != null)
     {
@@ -338,26 +263,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
-  public JComboBox<String> getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setThreshold(JComboBox<String> threshold)
-  {
-    this.threshold = threshold;
-  }
-
-  public JComboBox<String> getAnnotations()
-  {
-    return annotations;
-  }
-
-  public void setAnnotations(JComboBox<String> annotations)
-  {
-    this.annotations = annotations;
-  }
-
   @Override
   public void updateView()
   {
@@ -568,6 +473,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     selectedAnnotationChanged();
   }
 
+  @Override
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
@@ -585,6 +491,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ngFurtherActionPanel.syncState();
     ngStructureFilterPanel.syncState();
 
+    CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+            .getLayout();
     switchableViewsLayout.show(switchableViewsPanel, currentView);
     updateView();
   }
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index b1f0edb..84f3e6c 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -55,7 +55,6 @@ import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
@@ -708,7 +707,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int column = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -905,7 +905,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
+            * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -946,7 +947,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       imageFresh = true;
     }
 
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -976,8 +978,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.startRes;
-    int er = av.endRes + 1;
+    int sr = av.getRanges().getStartRes();
+    int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 166e1ad..c2bf41b 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -22,12 +22,21 @@ package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
 import javax.swing.JButton;
@@ -49,22 +58,10 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected int[] annmap;
 
-  protected boolean enableSeqAss = false;
-
-  private AlignmentAnnotation currentAnnotation;
-
   protected boolean adjusting = false;
 
-  protected JCheckBox currentColours = new JCheckBox();
-
-  protected JPanel minColour = new JPanel();
-
-  protected JPanel maxColour = new JPanel();
-
   protected JCheckBox seqAssociated = new JCheckBox();
 
-  protected JCheckBox thresholdIsMin = new JCheckBox();
-
   protected JSlider slider = new JSlider();
 
   protected JTextField thresholdValue = new JTextField(20);
@@ -81,6 +78,38 @@ public abstract class AnnotationRowFilter extends JPanel
    */
   protected boolean sliderDragging = false;
 
+  protected JComboBox<String> threshold = new JComboBox<String>();
+
+  protected JComboBox<String> annotations;
+
+  /*
+   * map from annotation to its menu item display label
+   * - so we know which item to pre-select on restore
+   */
+  private Map<AlignmentAnnotation, String> annotationLabels;
+
+  private AlignmentAnnotation currentAnnotation;
+
+  /**
+   * Constructor
+   * 
+   * @param viewport
+   * @param alignPanel
+   */
+  public AnnotationRowFilter(AlignViewport viewport, final AlignmentPanel alignPanel)
+  {
+    this.av = viewport;
+    this.ap = alignPanel;
+    thresholdValue.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
+  }
+
   protected void addSliderChangeListener()
   {
 
@@ -130,25 +159,27 @@ public abstract class AnnotationRowFilter extends JPanel
     });
   }
 
-  public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
-  {
-    this.av = av;
-    this.ap = ap;
-  }
-
-  public AnnotationRowFilter()
-  {
-
-  }
-
+/**
+ * Builds and returns a list of menu items (display text) for choice of
+ * annotation. Also builds maps between annotations, their positions in the
+ * list, and their display labels in the list.
+ * 
+ * @param isSeqAssociated
+ * @return
+ */
   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
   {
+    annotationLabels = new HashMap<AlignmentAnnotation, String>();
+
     Vector<String> list = new Vector<String>();
     int index = 1;
     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+    seqAssociated.setEnabled(false);
     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
     {
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
+      AlignmentAnnotation annotation = av.getAlignment()
+              .getAlignmentAnnotation()[i];
+      if (annotation.sequenceRef == null)
       {
         if (isSeqAssociated)
         {
@@ -157,30 +188,29 @@ public abstract class AnnotationRowFilter extends JPanel
       }
       else
       {
-        enableSeqAss = true;
+        seqAssociated.setEnabled(true);
       }
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = annotation.label;
       // add associated sequence ID if available
-      if (!isSeqAssociated
-              && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      if (!isSeqAssociated && annotation.sequenceRef != null)
       {
-        label = label
-                + "_"
-                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
-                        .getName();
+        label = label + "_" + annotation.sequenceRef.getName();
       }
       // make label unique
       if (!list.contains(label))
       {
         anmap[list.size()] = i;
         list.add(label);
+        annotationLabels.put(annotation, label);
       }
       else
       {
         if (!isSeqAssociated)
         {
           anmap[list.size()] = i;
-          list.add(label + "_" + (index++));
+          label = label + "_" + (index++);
+          list.add(label);
+          annotationLabels.put(annotation, label);
         }
       }
     }
@@ -203,11 +233,6 @@ public abstract class AnnotationRowFilter extends JPanel
     return selectedThresholdItem;
   }
 
-  public void modelChanged()
-  {
-    seqAssociated.setEnabled(enableSeqAss);
-  }
-
   public void ok_actionPerformed()
   {
     try
@@ -230,22 +255,22 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdCheck_actionPerformed()
+  protected void thresholdCheck_actionPerformed()
   {
     updateView();
   }
 
-  public void annotations_actionPerformed()
+  protected void selectedAnnotationChanged()
   {
     updateView();
   }
 
-  public void threshold_actionPerformed()
+  protected void threshold_actionPerformed()
   {
     updateView();
   }
 
-  public void thresholdValue_actionPerformed()
+  protected void thresholdValue_actionPerformed()
   {
     try
     {
@@ -257,27 +282,34 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  public void thresholdIsMin_actionPerformed()
+  protected void thresholdIsMin_actionPerformed()
   {
     updateView();
   }
 
-  protected void populateThresholdComboBox(JComboBox<String> threshold)
+  protected void populateThresholdComboBox(JComboBox<String> thresh)
   {
-    threshold.addItem(MessageManager
+    thresh.addItem(MessageManager
             .getString("label.threshold_feature_no_threshold"));
-    threshold.addItem(MessageManager
+    thresh.addItem(MessageManager
             .getString("label.threshold_feature_above_threshold"));
-    threshold.addItem(MessageManager
+    thresh.addItem(MessageManager
             .getString("label.threshold_feature_below_threshold"));
   }
 
-  protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
+  /**
+   * Rebuilds the drop-down list of annotations to choose from when the 'per
+   * sequence only' checkbox is checked or unchecked.
+   * 
+   * @param anns
+   */
+  protected void seqAssociated_actionPerformed(JComboBox<String> anns)
   {
     adjusting = true;
-    String cursel = (String) annotations.getSelectedItem();
-    boolean isvalid = false, isseqs = seqAssociated.isSelected();
-    annotations.removeAllItems();
+    String cursel = (String) anns.getSelectedItem();
+    boolean isvalid = false;
+    boolean isseqs = seqAssociated.isSelected();
+    anns.removeAllItems();
     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
     {
       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
@@ -285,20 +317,22 @@ public abstract class AnnotationRowFilter extends JPanel
         isvalid = true;
         cursel = anitem;
       }
-      annotations.addItem(anitem);
+      anns.addItem(anitem);
     }
-    adjusting = false;
     if (isvalid)
     {
-      annotations.setSelectedItem(cursel);
+      anns.setSelectedItem(cursel);
     }
     else
     {
-      if (annotations.getItemCount() > 0)
+      if (anns.getItemCount() > 0)
       {
-        annotations.setSelectedIndex(0);
+        anns.setSelectedIndex(0);
       }
     }
+    adjusting = false;
+
+    updateView();
   }
 
   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
@@ -329,76 +363,107 @@ public abstract class AnnotationRowFilter extends JPanel
     }
   }
 
-  protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
-          int selectedThresholdOption)
+  public AlignmentAnnotation getCurrentAnnotation()
   {
+    return currentAnnotation;
+  }
 
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-    {
-      acg = new AnnotationColourGradient(currentAnn,
-              av.getGlobalColourScheme(), selectedThresholdOption);
-    }
-    else
-    {
-      acg = new AnnotationColourGradient(currentAnn,
-              minColour.getBackground(), maxColour.getBackground(),
-              selectedThresholdOption);
-    }
-    acg.setSeqAssociated(seqAssociated.isSelected());
+  protected void setCurrentAnnotation(AlignmentAnnotation annotation)
+  {
+    this.currentAnnotation = annotation;
+  }
 
-    if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
-    {
-      acg.setPredefinedColours(true);
-    }
+  protected abstract void valueChanged(boolean updateAllAnnotation);
+
+  protected abstract void updateView();
 
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+  protected abstract void reset();
 
-    av.setGlobalColourScheme(acg);
+  protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
+  {
+    return annotationLabels.get(ann);
+  }
 
-    if (av.getAlignment().getGroups() != null)
+  protected void jbInit()
+  {
+    ok.setOpaque(false);
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
     {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed();
+      }
+    });
 
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+    cancel.setOpaque(false);
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
-        if (sg.cs == null)
-        {
-          continue;
-        }
+        cancel_actionPerformed();
+      }
+    });
 
-        AnnotationColourGradient scheme = null;
-        if (currentColours.isSelected())
-        {
-          scheme = new AnnotationColourGradient(currentAnn,
-                  sg.getColourScheme(), selectedThresholdOption);
-        }
-        else
-        {
-          scheme = new AnnotationColourGradient(currentAnn,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdOption);
-        }
-        scheme.setSeqAssociated(seqAssociated.isSelected());
-        sg.setColourScheme(scheme);
+    annotations.addItemListener(new ItemListener()
+    {
+      @Override
+      public void itemStateChanged(ItemEvent e)
+      {
+        selectedAnnotationChanged();
       }
-    }
-    return false;
+    });
+    annotations.setToolTipText(MessageManager
+            .getString("info.select_annotation_row"));
+
+    threshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed();
+      }
+    });
+
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed();
+      }
+    });
+
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(100, 32));
   }
 
-  public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+  public JComboBox<String> getThreshold()
   {
-    return currentAnnotation;
+    return threshold;
   }
 
-  public void setCurrentAnnotation(
-          jalview.datamodel.AlignmentAnnotation currentAnnotation)
+  public void setThreshold(JComboBox<String> thresh)
   {
-    this.currentAnnotation = currentAnnotation;
+    this.threshold = thresh;
   }
 
-  public abstract void valueChanged(boolean updateAllAnnotation);
-
-  public abstract void updateView();
+  public JComboBox<String> getAnnotations()
+  {
+    return annotations;
+  }
 
-  public abstract void reset();
+  public void setAnnotations(JComboBox<String> anns)
+  {
+    this.annotations = anns;
+  }
 }
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index ffb9639..5d23f49 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -45,7 +45,6 @@ import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
-import javax.swing.JMenu;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -147,7 +146,7 @@ public class AppJmol extends StructureViewerBase
   {
     super.initMenus();
 
-    viewerActionMenu = new JMenu(MessageManager.getString("label.jmol"));
+    viewerActionMenu.setText(MessageManager.getString("label.jmol"));
 
     viewerColour
             .setText(MessageManager.getString("label.colour_with_jmol"));
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 75e0c5e..f822358 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -40,8 +40,6 @@ public class AppJmolBinding extends JalviewJmolBinding
 {
   private AppJmol appJmolWindow;
 
-  private FeatureRenderer fr = null;
-
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
   {
@@ -50,26 +48,6 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow
-            .getAlignmentPanel() : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      if (fr == null)
-      {
-        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
-    }
-
-    return fr;
-  }
-
-  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -215,4 +193,18 @@ public class AppJmolBinding extends JalviewJmolBinding
   {
     return appJmolWindow;
   }
+
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
+  {
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow
+            .getAlignmentPanel() : (AlignmentPanel) alignment;
+    if (ap.av.isShowSequenceFeatures())
+    {
+      return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
+    }
+
+    return null;
+  }
 }
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 530f4fe..ec9feb7 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -20,10 +20,12 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureRenderer;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraCommands;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
@@ -35,16 +37,22 @@ import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
 
 import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 import java.util.Random;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JInternalFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
@@ -58,8 +66,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 {
   private JalviewChimeraBinding jmb;
 
-  private boolean allChainsSelected = false;
-
   private IProgressIndicator progressBar = null;
 
   /*
@@ -71,6 +77,10 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   private Random random = new Random();
 
+  private int myWidth = 500;
+
+  private int myHeight = 150;
+
   /**
    * Initialise menu options.
    */
@@ -89,6 +99,100 @@ public class ChimeraViewFrame extends StructureViewerBase
     helpItem.setText(MessageManager.getString("label.chimera_help"));
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
+
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_chimera_attributes"));
+    writeFeatures.setToolTipText(MessageManager
+            .getString("label.create_chimera_attributes_tip"));
+    writeFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sendFeaturesToChimera();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
+
+    final JMenu fetchAttributes = new JMenu(
+            MessageManager.getString("label.fetch_chimera_attributes"));
+    fetchAttributes.setToolTipText(MessageManager
+            .getString("label.fetch_chimera_attributes_tip"));
+    fetchAttributes.addMouseListener(new MouseAdapter()
+    {
+
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        buildAttributesMenu(fetchAttributes);
+      }
+    });
+    viewerActionMenu.add(fetchAttributes);
+
+  }
+
+  /**
+   * Query Chimera for its residue attribute names and add them as items off the
+   * attributes menu
+   * 
+   * @param attributesMenu
+   */
+  protected void buildAttributesMenu(JMenu attributesMenu)
+  {
+    List<String> atts = jmb.sendChimeraCommand("list resattr", true);
+    if (atts == null)
+    {
+      return;
+    }
+    attributesMenu.removeAll();
+    Collections.sort(atts);
+    for (String att : atts)
+    {
+      final String attName = att.split(" ")[1];
+
+      /*
+       * ignore 'jv_*' attributes, as these are Jalview features that have
+       * been transferred to residue attributes in Chimera!
+       */
+      if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
+      {
+        JMenuItem menuItem = new JMenuItem(attName);
+        menuItem.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            getChimeraAttributes(attName);
+          }
+        });
+        attributesMenu.add(menuItem);
+      }
+    }
+  }
+
+  /**
+   * Read residues in Chimera with the given attribute name, and set as features
+   * on the corresponding sequence positions (if any)
+   * 
+   * @param attName
+   */
+  protected void getChimeraAttributes(String attName)
+  {
+    jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
+  }
+
+  /**
+   * Send a command to Chimera to create residue attributes for Jalview features
+   * <p>
+   * The syntax is: setattr r <attName> <attValue> <atomSpec>
+   * <p>
+   * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+   */
+  protected void sendFeaturesToChimera()
+  {
+    int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
+    statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+            count));
   }
 
   /**
@@ -146,7 +250,6 @@ public class ChimeraViewFrame extends StructureViewerBase
           SequenceI[][] seqs)
   {
     createProgressBar();
-    // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
     jmb = new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, null);
     addAlignmentPanel(ap);
@@ -158,7 +261,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       useAlignmentPanelForSuperposition(ap);
     }
     jmb.setColourBySequence(true);
-    setSize(400, 400); // probably should be a configurable/dynamic default here
+    setSize(myWidth, myHeight);
     initMenus();
 
     addingStructures = false;
@@ -270,7 +373,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   void initChimera()
   {
     jmb.setFinishedInit(false);
-    jalview.gui.Desktop.addInternalFrame(this,
+    Desktop.addInternalFrame(this,
             jmb.getViewerTitle(getViewerName(), true), getBounds().width,
             getBounds().height);
 
@@ -294,12 +397,10 @@ public class ChimeraViewFrame extends StructureViewerBase
                         + chimeraSessionFile);
       }
     }
-    jmb.setFinishedInit(true);
 
     jmb.startChimeraListener();
   }
 
-
   /**
    * Show only the selected chain(s) in the viewer
    */
@@ -450,6 +551,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     if (files.length() > 0)
     {
+      jmb.setFinishedInit(false);
       if (!addingStructures)
       {
         try
@@ -507,10 +609,21 @@ public class ChimeraViewFrame extends StructureViewerBase
           }
         }
       }
+
       jmb.refreshGUI();
       jmb.setFinishedInit(true);
       jmb.setLoadingFromArchive(false);
 
+      /*
+       * ensure that any newly discovered features (e.g. RESNUM)
+       * are added to any open feature settings dialog
+       */
+      FeatureRenderer fr = getBinding().getFeatureRenderer(null);
+      if (fr != null)
+      {
+        fr.featuresAdded();
+      }
+
       // refresh the sequence colours for the new structure(s)
       for (AlignmentPanel ap : _colourwith)
       {
@@ -656,7 +769,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     {
       BrowserLauncher
               .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
-    } catch (Exception ex)
+    } catch (IOException ex)
     {
     }
   }
@@ -754,4 +867,20 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     return "Chimera";
   }
+
+  /**
+   * Sends commands to align structures according to associated alignment(s).
+   * 
+   * @return
+   */
+  @Override
+  protected String alignStructs_withAllAlignPanels()
+  {
+    String reply = super.alignStructs_withAllAlignPanels();
+    if (reply != null)
+    {
+      statusBar.setText("Superposition failed: " + reply);
+    }
+    return reply;
+  }
 }
diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index 31780d6..19ad939 100644
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -3,6 +3,7 @@ package jalview.gui;
 import jalview.bin.Cache;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
@@ -258,7 +259,7 @@ public class ColourMenuHelper
     {
       try
       {
-        UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+        UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
         if (ucs != null
                 && ColourSchemes.getInstance().nameExists(ucs.getName()))
         {
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index ed6a3c5..f519f99 100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -46,7 +46,6 @@ import java.util.Comparator;
 import javax.swing.JColorChooser;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JSpinner;
@@ -61,8 +60,7 @@ import javax.swing.SwingConstants;
  * @version $Revision$
  */
 public class FeatureRenderer extends
-        jalview.renderer.seqfeatures.FeatureRenderer implements
-        jalview.api.FeatureRenderer
+        jalview.renderer.seqfeatures.FeatureRenderer
 {
   Color resBoxColour;
 
@@ -339,9 +337,6 @@ public class FeatureRenderer extends
 
     if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
     {
-      // This ensures that the last sequence
-      // is refreshed and new features are rendered
-      lastSeq = null;
       lastFeatureAdded = name.getText().trim();
       lastFeatureGroupAdded = source.getText().trim();
       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 37be8bc..aad0776 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -158,33 +159,35 @@ public class IdCanvas extends JPanel
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transY = 0;
 
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - (vertical * av.getCharHeight());
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
-    else if (vertical < 0)
+    else if (vertical < 0) // scroll up
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -240,7 +243,7 @@ public class IdCanvas extends JPanel
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
 
-    drawIds(av.getStartSeq(), av.endSeq);
+    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
 
     g.drawImage(image, 0, 0, this);
   }
@@ -314,10 +317,11 @@ public class IdCanvas extends JPanel
 
       int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
 
-      int rowSize = av.getEndRes() - av.getStartRes();
+      int rowSize = av.getRanges().getEndRes()
+              - av.getRanges().getStartRes();
 
       // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+      for (int ypos = hgap, row = av.getRanges().getStartRes(); (ypos <= getHeight())
               && (row < maxwidth); ypos += cHeight, row += rowSize)
       {
         for (int i = starty; i < alheight; i++)
@@ -354,7 +358,7 @@ public class IdCanvas extends JPanel
 
       SequenceI sequence;
       // Now draw the id strings
-      for (int i = starty; i < endy; i++)
+      for (int i = starty; i <= endy; i++)
       {
         sequence = av.getAlignment().getSequenceAt(i);
 
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 6ae19f0..2074900 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -242,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    if (mouseDragging && (e.getY() < 0)
+            && (av.getRanges().getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.getAlignment().getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -442,9 +443,10 @@ public class IdPanel extends JPanel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getRanges().getStartSeq() > index)
+            || (av.getRanges().getEndSeq() < index))
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
     }
   }
 
@@ -486,11 +488,11 @@ public class IdPanel extends JPanel implements MouseListener,
         if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
 
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3ac453f..c19f005 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceGroup;
@@ -77,7 +78,6 @@ import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
@@ -87,6 +87,7 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -755,6 +756,7 @@ public class Jalview2XML
     List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
 
     AlignViewport av = ap.av;
+    ViewportRanges vpRanges = av.getRanges();
 
     JalviewModel object = new JalviewModel();
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
@@ -1270,8 +1272,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.startRes);
-      view.setStartSeq(av.startSeq);
+      view.setStartRes(vpRanges.getStartRes());
+      view.setStartSeq(vpRanges.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
@@ -1711,6 +1713,15 @@ public class Jalview2XML
     return matchedFile;
   }
 
+  /**
+   * Populates the AnnotationColours xml for save. This captures the settings of
+   * the options in the 'Colour by Annotation' dialog.
+   * 
+   * @param acg
+   * @param userColours
+   * @param jms
+   * @return
+   */
   private AnnotationColours constructAnnotationColours(
           AnnotationColourGradient acg, List<UserColourScheme> userColours,
           JalviewModelSequence jms)
@@ -1718,8 +1729,9 @@ public class Jalview2XML
     AnnotationColours ac = new AnnotationColours();
     ac.setAboveThreshold(acg.getAboveThreshold());
     ac.setThreshold(acg.getAnnotationThreshold());
-    ac.setAnnotation(acg.getAnnotation());
-    if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+    // 2.10.2 save annotationId (unique) not annotation label
+    ac.setAnnotation(acg.getAnnotation().annotationId);
+    if (acg.getBaseColour() instanceof UserColourScheme)
     {
       ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
               userColours, jms));
@@ -2639,10 +2651,12 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    finalErrorMessage, "Error "
-                            + (saving ? "saving" : "loading")
-                            + " Jalview file", JvOptionPane.WARNING_MESSAGE);
+            JvOptionPane
+                    .showInternalMessageDialog(Desktop.desktop,
+                            finalErrorMessage, "Error "
+                                    + (saving ? "saving" : "loading")
+                                    + " Jalview file",
+                            JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -4448,8 +4462,8 @@ public class Jalview2XML
     af.viewport.setThresholdTextColour(view.getTextColThreshold());
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes
@@ -4689,12 +4703,21 @@ public class Jalview2XML
     return af;
   }
 
+  /**
+   * Reads saved data to restore Colour by Annotation settings
+   * 
+   * @param viewAnnColour
+   * @param af
+   * @param al
+   * @param jms
+   * @param checkGroupAnnColour
+   * @return
+   */
   private ColourSchemeI constructAnnotationColour(
           AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
           JalviewModelSequence jms, boolean checkGroupAnnColour)
   {
     boolean propagateAnnColour = false;
-    ColourSchemeI cs = null;
     AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
     if (checkGroupAnnColour && al.getGroups() != null
             && al.getGroups().size() > 0)
@@ -4702,7 +4725,7 @@ public class Jalview2XML
       // pre 2.8.1 behaviour
       // check to see if we should transfer annotation colours
       propagateAnnColour = true;
-      for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+      for (SequenceGroup sg : al.getGroups())
       {
         if (sg.getColourScheme() instanceof AnnotationColourGradient)
         {
@@ -4710,107 +4733,84 @@ public class Jalview2XML
         }
       }
     }
-    // int find annotation
-    if (annAlignment.getAlignmentAnnotation() != null)
+
+    /*
+     * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
+     */
+    String annotationId = viewAnnColour.getAnnotation();
+    AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
+
+    /*
+     * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
+     */
+    if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null)
     {
       for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
       {
-        if (annAlignment.getAlignmentAnnotation()[i].label
-                .equals(viewAnnColour.getAnnotation()))
+        if (annotationId
+                .equals(annAlignment.getAlignmentAnnotation()[i].label))
         {
-          if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
-          {
-            annAlignment.getAlignmentAnnotation()[i]
-                    .setThreshold(new jalview.datamodel.GraphLine(
-                            viewAnnColour.getThreshold(), "Threshold",
-                            java.awt.Color.black)
-
-                    );
-          }
-
-          if (viewAnnColour.getColourScheme().equals(
-                  ResidueColourScheme.NONE))
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    new java.awt.Color(viewAnnColour.getMinColour()),
-                    new java.awt.Color(viewAnnColour.getMaxColour()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          else if (viewAnnColour.getColourScheme().startsWith("ucs"))
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    getUserColourScheme(jms,
-                            viewAnnColour.getColourScheme()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          else
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    ColourSchemeProperty.getColourScheme(al,
-                            viewAnnColour.getColourScheme()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          if (viewAnnColour.hasPerSequence())
-          {
-            ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
-                    .isPerSequence());
-          }
-          if (viewAnnColour.hasPredefinedColours())
-          {
-            ((AnnotationColourGradient) cs)
-                    .setPredefinedColours(viewAnnColour
-                            .isPredefinedColours());
-          }
-          if (propagateAnnColour && al.getGroups() != null)
-          {
-            // Also use these settings for all the groups
-            for (int g = 0; g < al.getGroups().size(); g++)
-            {
-              jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
-
-              if (sg.cs == null)
-              {
-                continue;
-              }
+          matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
+          break;
+        }
+      }
+    }
+    if (matchedAnnotation == null)
+    {
+      System.err.println("Failed to match annotation colour scheme for "
+              + annotationId);
+      return null;
+    }
+    if (matchedAnnotation.getThreshold() == null)
+    {
+      matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
+              "Threshold", Color.black));
+    }
 
-              /*
-               * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs =
-               * new AnnotationColourGradient(
-               * annAlignment.getAlignmentAnnotation()[i], new
-               * java.awt.Color(viewAnnColour. getMinColour()), new
-               * java.awt.Color(viewAnnColour. getMaxColour()),
-               * viewAnnColour.getAboveThreshold()); } else
-               */
-              {
-                sg.setColourScheme(new AnnotationColourGradient(
-                        annAlignment.getAlignmentAnnotation()[i], sg
-                                .getColourScheme(), viewAnnColour
-                                .getAboveThreshold()));
-                if (cs instanceof AnnotationColourGradient)
-                {
-                  if (viewAnnColour.hasPerSequence())
-                  {
-                    ((AnnotationColourGradient) cs)
-                            .setSeqAssociated(viewAnnColour.isPerSequence());
-                  }
-                  if (viewAnnColour.hasPredefinedColours())
-                  {
-                    ((AnnotationColourGradient) cs)
-                            .setPredefinedColours(viewAnnColour
-                                    .isPredefinedColours());
-                  }
-                }
-              }
+    AnnotationColourGradient cs = null;
+    if (viewAnnColour.getColourScheme().equals("None"))
+    {
+      cs = new AnnotationColourGradient(matchedAnnotation, new Color(
+              viewAnnColour.getMinColour()), new Color(
+              viewAnnColour.getMaxColour()),
+              viewAnnColour.getAboveThreshold());
+    }
+    else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+    {
+      cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(
+              jms, viewAnnColour.getColourScheme()),
+              viewAnnColour.getAboveThreshold());
+    }
+    else
+    {
+      cs = new AnnotationColourGradient(matchedAnnotation,
+              ColourSchemeProperty.getColourScheme(al,
+                      viewAnnColour.getColourScheme()),
+              viewAnnColour.getAboveThreshold());
+    }
 
-            }
-          }
+    boolean perSequenceOnly = viewAnnColour.isPerSequence();
+    boolean useOriginalColours = viewAnnColour.isPredefinedColours();
+    cs.setSeqAssociated(perSequenceOnly);
+    cs.setPredefinedColours(useOriginalColours);
 
-          break;
+    if (propagateAnnColour && al.getGroups() != null)
+    {
+      // Also use these settings for all the groups
+      for (int g = 0; g < al.getGroups().size(); g++)
+      {
+        SequenceGroup sg = al.getGroups().get(g);
+        if (sg.getGroupColourScheme() == null)
+        {
+          continue;
         }
 
+        AnnotationColourGradient groupScheme = new AnnotationColourGradient(
+                matchedAnnotation, sg.getColourScheme(),
+                viewAnnColour.getAboveThreshold());
+        sg.setColourScheme(groupScheme);
+        groupScheme.setSeqAssociated(perSequenceOnly);
+        groupScheme.setPredefinedColours(useOriginalColours);
       }
     }
     return cs;
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index e751a2c..6235cbe 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -367,8 +367,8 @@ public class Jalview2XML_V1
 
     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
             view.getHeight());
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+    af.viewport.getRanges().setStartSeq(view.getStartSeq());
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
     af.viewport.setColourText(view.getShowColourText());
diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index a797872..c9b35d8 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -28,13 +28,12 @@ import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
+import javax.swing.SwingUtilities;
+
 public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 {
   private ChimeraViewFrame cvf;
 
-  private FeatureRenderer fr = null;
-
-
   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
           SequenceI[][] sequenceIs, DataSourceType protocol)
@@ -50,17 +49,10 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
             : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
-      if (fr == null)
-      {
-        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
+      return ap.getSeqPanel().seqCanvas.fr;
     }
 
-    return fr;
+    return null;
   }
 
   @Override
@@ -122,24 +114,25 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   protected void sendAsynchronousCommand(final String command,
           final String progressMsg)
   {
-    Thread thread = new Thread(new Runnable()
+    final long handle = progressMsg == null ? 0 : cvf
+            .startProgressBar(progressMsg);
+    SwingUtilities.invokeLater(new Runnable()
     {
-
       @Override
       public void run()
       {
-        long stm = cvf.startProgressBar(progressMsg);
         try
         {
           sendChimeraCommand(command, false);
         } finally
         {
-          cvf.stopProgressBar(null, stm);
+          if (progressMsg != null)
+          {
+            cvf.stopProgressBar(null, handle);
+          }
         }
       }
     });
-    thread.start();
-
   }
 
   @Override
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 1c48690..c530fdc 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,7 +20,10 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.viewmodel.OverviewDimensions;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -35,57 +38,51 @@ import java.awt.image.BufferedImage;
 import javax.swing.JPanel;
 
 /**
- * DOCUMENT ME!
+ * Panel displaying an overview of the full alignment, with an interactive box
+ * representing the viewport onto the alignment.
  * 
  * @author $author$
  * @version $Revision$
  */
 public class OverviewPanel extends JPanel implements Runnable
 {
-  BufferedImage miniMe;
+  private static final Color TRANS_GREY = new Color(100, 100, 100, 25);
 
-  AlignViewport av;
+  private final AnnotationRenderer renderer = new AnnotationRenderer();
 
-  AlignmentPanel ap;
+  private OverviewDimensions od;
 
-  final AnnotationRenderer renderer = new AnnotationRenderer();
+  private BufferedImage miniMe;
 
-  float scalew = 1f;
-
-  float scaleh = 1f;
-
-  int width;
-
-  int sequencesHeight;
-
-  int graphHeight = 20;
-
-  int boxX = -1;
+  private BufferedImage lastMiniMe = null;
 
-  int boxY = -1;
+  private AlignViewport av;
 
-  int boxWidth = -1;
+  private AlignmentPanel ap;
 
-  int boxHeight = -1;
+  //
+  private boolean resizing = false;
 
-  boolean resizing = false;
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  private boolean resizeAgain = false;
 
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
-  SequenceRenderer sr;
+  private SequenceRenderer sr;
 
   jalview.renderer.seqfeatures.FeatureRenderer fr;
 
   /**
    * Creates a new OverviewPanel object.
    * 
-   * @param ap
-   *          DOCUMENT ME!
+   * @param alPanel
+   *          The alignment panel which is shown in the overview panel
    */
-  public OverviewPanel(AlignmentPanel ap)
+  public OverviewPanel(AlignmentPanel alPanel)
   {
-    this.av = ap.av;
-    this.ap = ap;
+    this.av = alPanel.av;
+    this.ap = alPanel;
     setLayout(null);
 
     sr = new SequenceRenderer(av);
@@ -93,44 +90,17 @@ public class OverviewPanel extends JPanel implements Runnable
     sr.forOverview = true;
     fr = new FeatureRenderer(ap);
 
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.getAlignment().getWidth()
-            / (float) av.getAlignment().getHeight();
-
-    if (av.getAlignmentConservationAnnotation() == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
+    od = new OverviewDimensions(av.getRanges(),
+            (av.isShowAnnotation() && av
+                    .getAlignmentConservationAnnotation() != null));
 
     addComponentListener(new ComponentAdapter()
     {
       @Override
       public void componentResized(ComponentEvent evt)
       {
-        if ((getWidth() != width)
-                || (getHeight() != (sequencesHeight + graphHeight)))
+        if ((getWidth() != od.getWidth())
+                || (getHeight() != (od.getHeight())))
         {
           updateOverviewImage();
         }
@@ -144,11 +114,10 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          // TODO: feature: jv2.5 detect shift drag and update selection from
-          // it.
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getRanges());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -160,9 +129,10 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         if (!av.getWrapAlignment())
         {
-          boxX = evt.getX();
-          boxY = evt.getY();
-          checkValid();
+          od.updateViewportFromMouse(evt.getX(), evt.getY(), av
+                  .getAlignment().getHiddenSequences(), av
+                  .getColumnSelection(), av.getRanges());
+          ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
         }
       }
     });
@@ -171,60 +141,7 @@ public class OverviewPanel extends JPanel implements Runnable
   }
 
   /**
-   * DOCUMENT ME!
-   */
-  void checkValid()
-  {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns())
-      {
-        // Try smallest possible box
-        boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns())
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows())
-    {
-      row = av.getAlignment().getHiddenSequences()
-              .findIndexWithoutHiddenSeqs(row);
-    }
-
-    ap.setScrollValues(col, row);
-
-  }
-
-  /**
-   * DOCUMENT ME!
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -238,24 +155,17 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if ((getWidth() > 0) && (getHeight() > 0))
     {
-      width = getWidth();
-      sequencesHeight = getHeight() - graphHeight;
+      od.setWidth(getWidth());
+      od.setHeight(getHeight());
     }
 
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
     Thread thread = new Thread(this);
     thread.start();
     repaint();
   }
 
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
-  /**
-   * DOCUMENT ME!
-   */
   @Override
   public void run()
   {
@@ -266,148 +176,47 @@ public class OverviewPanel extends JPanel implements Runnable
       fr.transferSettings(ap.getSeqPanel().seqCanvas.getFeatureRenderer());
     }
 
-    int alwidth = av.getAlignment().getWidth();
-    int alheight = av.getAlignment().getHeight()
-            + av.getAlignment().getHiddenSequences().getSize();
-
-    setPreferredSize(new Dimension(width, sequencesHeight + graphHeight));
-
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
+    // why do we need to set preferred size again? was set in
+    // updateOverviewImage
+    setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = new BufferedImage(width, sequencesHeight + graphHeight,
+    miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
             BufferedImage.TYPE_INT_RGB);
 
     Graphics mg = miniMe.getGraphics();
     mg.setColor(Color.orange);
-    mg.fillRect(0, 0, width, miniMe.getHeight());
-
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
+    mg.fillRect(0, 0, od.getWidth(), miniMe.getHeight());
 
-    int lastcol = -1, lastrow = -1;
-    int color = Color.white.getRGB();
-    int row, col;
-    jalview.datamodel.SequenceI seq;
-    final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
-            .hasHiddenColumns();
-    boolean hiddenRow = false;
-    // get hidden row and hidden column map once at beginning.
-    // clone featureRenderer settings to avoid race conditions... if state is
-    // updated just need to refresh again
-    for (row = 0; row < sequencesHeight; row++)
-    {
-      if (resizeAgain)
-      {
-        break;
-      }
-      if ((int) (row * sampleRow) == lastrow)
-      {
-        // No need to recalculate the colours,
-        // Just copy from the row above
-        for (col = 0; col < width; col++)
-        {
-          if (resizeAgain)
-          {
-            break;
-          }
-          miniMe.setRGB(col, row, miniMe.getRGB(col, row - 1));
-        }
-        continue;
-      }
-
-      lastrow = (int) (row * sampleRow);
-
-      hiddenRow = false;
-      if (hasHiddenRows)
-      {
-        seq = av.getAlignment().getHiddenSequences()
-                .getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index = av.getAlignment().getHiddenSequences()
-                  .findIndexWithoutHiddenSeqs(lastrow);
-
-          seq = av.getAlignment().getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = av.getAlignment().getSequenceAt(lastrow);
-      }
-
-      if (seq == null)
-      {
-        System.out.println(lastrow + " null");
-        continue;
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if (resizeAgain)
-        {
-          break;
-        }
-        if ((int) (col * sampleCol) == lastcol
-                && (int) (row * sampleRow) == lastrow)
-        {
-          miniMe.setRGB(col, row, color);
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(seq, lastcol).getRGB();
-
-          if (av.isShowSequenceFeatures())
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = -1; // White
-        }
+    // calculate sampleCol and sampleRow
+    // alignment width is max number of residues/bases
+    // alignment height is number of sequences
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getAbsoluteHeight();
 
-        if (hiddenRow
-                || (hasHiddenCols && !av.getColumnSelection().isVisible(
-                        lastcol)))
-        {
-          color = new Color(color).darker().darker().getRGB();
-        }
+    // sampleCol or sampleRow is the width/height allocated to each residue
+    // in particular, sometimes we may need more than one row/col of the
+    // BufferedImage allocated
+    // sampleCol is how much of a residue to assign to each pixel
+    // sampleRow is how many sequences to assign to each pixel
+    float sampleCol = alwidth / (float) od.getWidth();
+    float sampleRow = alheight / (float) od.getSequencesHeight();
 
-        miniMe.setRGB(col, row, color);
+    buildImage(sampleRow, sampleCol);
 
-      }
-    }
-
-    if (av.getAlignmentConservationAnnotation() != null)
+    // check for conservation annotation to make sure overview works for DNA too
+    if (av.isShowAnnotation()
+            && (av.getAlignmentConservationAnnotation() != null))
     {
       renderer.updateFromAlignViewport(av);
-      for (col = 0; col < width; col++)
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
-        if (resizeAgain)
-        {
-          break;
-        }
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-                  av.getAlignmentConservationAnnotation().annotations,
-                  (int) (sampleCol) + 1, graphHeight,
-                  (int) (col * sampleCol), (int) (col * sampleCol) + 1);
-          mg.translate(-col, -sequencesHeight);
-        }
+        mg.translate(col, od.getSequencesHeight());
+        renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+                av.getAlignmentConservationAnnotation().annotations,
+                (int) (sampleCol) + 1, od.getGraphHeight(),
+                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+        mg.translate(-col, -od.getSequencesHeight());
+
       }
     }
     System.gc();
@@ -427,66 +236,97 @@ public class OverviewPanel extends JPanel implements Runnable
     setBoxPosition();
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * Build the overview panel image
    */
-  public void setBoxPosition()
+  private void buildImage(float sampleRow, float sampleCol)
   {
-    int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
-            .getHiddenSequences().getSize())
-            * av.getCharHeight();
+    int lastcol = -1;
+    int lastrow = -1;
+    int rgbColour = Color.white.getRGB();
 
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
+    SequenceI seq = null;
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
 
-    if (av.hasHiddenColumns())
+    final boolean hasHiddenCols = av.hasHiddenColumns();
+    boolean hiddenRow = false;
+    // get hidden row and hidden column map once at beginning.
+    // clone featureRenderer settings to avoid race conditions... if state is
+    // updated just need to refresh again
+    for (int row = 0; row < od.getSequencesHeight() && !resizeAgain; row++)
     {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
+      boolean doCopy = true;
+      int currentrow = (int) (row * sampleRow);
+      if (currentrow != lastrow)
+      {
+        doCopy = false;
 
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
+        lastrow = currentrow;
 
-    if (av.hasHiddenRows())
-    {
-      startSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(startSeq);
+        // get the sequence which would be at alignment index 'lastrow' if no
+        // rows were hidden, and determine whether it is hidden or not
+        hiddenRow = av.getAlignment().isHidden(lastrow);
+        seq = av.getAlignment().getSequenceAtAbsoluteIndex(lastrow);
+      }
 
-      endSeq = av.getAlignment().getHiddenSequences()
-              .adjustForHiddenSeqs(endSeq);
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
+      {
+        if (doCopy)
+        {
+          rgbColour = miniMe.getRGB(col, row - 1);
+        }
+        else if ((int) (col * sampleCol) != lastcol
+                || (int) (row * sampleRow) != lastrow)
+        {
+          lastcol = (int) (col * sampleCol);
+          rgbColour = getColumnColourFromSequence(seq, hiddenRow,
+                  hasHiddenCols, lastcol, finder);
+        }
+        // else we just use the color we already have , so don't need to set it
 
+        miniMe.setRGB(col, row, rgbColour);
+      }
     }
+  }
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+  /*
+   * Find the colour of a sequence at a specified column position
+   */
+  private int getColumnColourFromSequence(
+          jalview.datamodel.SequenceI seq,
+          boolean hiddenRow, boolean hasHiddenCols, int lastcol,
+          FeatureColourFinder finder)
+  {
+    Color color = Color.white;
 
-    if (av.hasHiddenColumns())
+    if ((seq != null) && (seq.getLength() > lastcol))
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+    	color = sr.getResidueColour(seq, lastcol, finder);
     }
-    else
+
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = color.darker().darker();
     }
 
-    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
-
-    repaint();
+    return color.getRGB();
   }
 
-  private BufferedImage lastMiniMe = null;
-
   /**
-   * DOCUMENT ME!
+   * Update the overview panel box when the associated alignment panel is
+   * changed
    * 
-   * @param g
-   *          DOCUMENT ME!
    */
+  public void setBoxPosition()
+  {
+    od.setBoxPosition(av.getAlignment()
+            .getHiddenSequences(), av.getColumnSelection(), av.getRanges());
+    repaint();
+  }
+
+
   @Override
   public void paintComponent(Graphics g)
   {
@@ -501,7 +341,7 @@ public class OverviewPanel extends JPanel implements Runnable
       {
         g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
       }
-      g.setColor(new Color(100, 100, 100, 25));
+      g.setColor(TRANS_GREY);
       g.fillRect(0, 0, getWidth(), getHeight());
     }
     else if (lastMiniMe != null)
@@ -509,13 +349,12 @@ public class OverviewPanel extends JPanel implements Runnable
       g.drawImage(lastMiniMe, 0, 0, this);
       if (lastMiniMe != miniMe)
       {
-        g.setColor(new Color(100, 100, 100, 25));
+        g.setColor(TRANS_GREY);
         g.fillRect(0, 0, getWidth(), getHeight());
       }
     }
-    // TODO: render selected regions
+
     g.setColor(Color.red);
-    g.drawRect(boxX, boxY, boxWidth, boxHeight);
-    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+    od.drawBox(g);
   }
 }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 81c3d4f..d91fa70 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -43,7 +43,6 @@ import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
@@ -1179,12 +1178,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         hideInsertions_actionPerformed(e);
       }
     });
-    /*
-     * annotationMenuItem.setText("By Annotation");
-     * annotationMenuItem.addActionListener(new ActionListener() { public void
-     * actionPerformed(ActionEvent actionEvent) {
-     * annotationMenuItem_actionPerformed(actionEvent); } });
-     */
+
     groupMenu.add(sequenceSelDetails);
     add(groupMenu);
     add(sequenceMenu);
@@ -1620,24 +1614,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     refresh();
   }
 
-  public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
-  {
-    SequenceGroup sg = getGroup();
-    if (sg == null)
-    {
-      return;
-    }
-
-    AnnotationColourGradient acg = new AnnotationColourGradient(
-            sequence.getAnnotation()[0], null,
-            AnnotationColourGradient.NO_THRESHOLD);
-
-    acg.setPredefinedColours(true);
-    sg.setColourScheme(acg);
-
-    refresh();
-  }
-
   /**
    * DOCUMENT ME!
    * 
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 8961f21..de21be6 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -101,7 +101,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    int x = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int x = (evt.getX() / av.getCharWidth()) + av.getRanges().getStartRes();
     final int res;
 
     if (av.hasHiddenColumns())
@@ -282,7 +282,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   {
     mouseDragging = false;
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -337,7 +338,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
     mouseDragging = true;
     ColumnSelection cs = av.getColumnSelection();
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
     res = Math.max(0, res);
     res = cs.adjustForHiddenColumns(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
@@ -389,7 +391,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int res = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
@@ -419,7 +422,8 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
   @Override
   public void paintComponent(Graphics g)
   {
-    drawScale(g, av.getStartRes(), av.getEndRes(), getWidth(), getHeight());
+    drawScale(g, av.getRanges().getStartRes(), av.getRanges().getEndRes(),
+            getWidth(), getHeight());
   }
 
   // scalewidth will normally be screenwidth,
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d015292..4557819 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -26,6 +26,7 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -279,10 +280,11 @@ public class SeqCanvas extends JComponent
     gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
             imgHeight, -horizontal * charWidth, -vertical * charHeight);
 
-    int sr = av.startRes;
-    int er = av.endRes;
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    ViewportRanges ranges = av.getRanges();
+    int sr = ranges.getStartRes();
+    int er = ranges.getEndRes();
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transX = 0;
     int transY = 0;
 
@@ -300,22 +302,22 @@ public class SeqCanvas extends JComponent
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - (vertical * charHeight);
+        transY = imgHeight - ((vertical + 1) * charHeight);
       }
     }
     else if (vertical < 0)
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -395,13 +397,15 @@ public class SeqCanvas extends JComponent
     gg.setColor(Color.white);
     gg.fillRect(0, 0, imgWidth, imgHeight);
 
+    ViewportRanges ranges = av.getRanges();
     if (av.getWrapAlignment())
     {
-      drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
+      drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
     }
     else
     {
-      drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+      drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+              ranges.getStartSeq(), ranges.getEndSeq(), 0);
     }
 
     g.drawImage(lcimg, 0, 0, this);
@@ -503,7 +507,7 @@ public class SeqCanvas extends JComponent
 
     av.setWrappedWidth(cWidth);
 
-    av.endRes = av.startRes + cWidth;
+    av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth);
 
     int endx;
     int ypos = hgap;
@@ -718,7 +722,7 @@ public class SeqCanvas extends JComponent
 
     // / First draw the sequences
     // ///////////////////////////
-    for (int i = startSeq; i < endSeq; i++)
+    for (int i = startSeq; i <= endSeq; i++)
     {
       nextSeq = av.getAlignment().getSequenceAt(i);
       if (nextSeq == null)
@@ -733,7 +737,7 @@ public class SeqCanvas extends JComponent
       if (av.isShowSequenceFeatures())
       {
         fr.drawSequence(g, nextSeq, startRes, endRes, offset
-                + ((i - startSeq) * charHeight));
+                + ((i - startSeq) * charHeight), false);
       }
 
       // / Highlight search Results once all sequences have been drawn
@@ -802,7 +806,7 @@ public class SeqCanvas extends JComponent
         int top = -1;
         int bottom = -1;
 
-        for (i = startSeq; i < endSeq; i++)
+        for (i = startSeq; i <= endSeq; i++)
         {
           sx = (group.getStartRes() - startRes) * charWidth;
           sy = offset + ((i - startSeq) * charHeight);
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 37b4852..db7aa36 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -209,7 +209,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
 
       wrappedBlock = y / cHeight;
-      wrappedBlock += av.getStartRes() / cwidth;
+      wrappedBlock += av.getRanges().getStartRes() / cwidth;
 
       res = wrappedBlock * cwidth + x / av.getCharWidth();
 
@@ -222,11 +222,11 @@ public class SeqPanel extends JPanel implements MouseListener,
         // right-hand gutter
         x = seqCanvas.getX() + seqCanvas.getWidth();
       }
-      res = (x / av.getCharWidth()) + av.getStartRes();
-      if (res > av.getEndRes())
+      res = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+      if (res > av.getRanges().getEndRes())
       {
         // moused off right
-        res = av.getEndRes();
+        res = av.getRanges().getEndRes();
       }
     }
 
@@ -262,7 +262,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+      seq = Math.min((y / av.getCharHeight())
+              + av.getRanges().getStartSeq(),
+              av
               .getAlignment().getHeight() - 1);
     }
 
@@ -385,18 +387,18 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      while (seqCanvas.cursorY < av.startSeq)
+      while (seqCanvas.cursorY < av.getRanges().getStartSeq())
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
+      while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq())
       {
         ap.scrollUp(false);
       }
       if (!av.getWrapAlignment())
       {
         while (seqCanvas.cursorX < av.getColumnSelection()
-                .adjustForHiddenColumns(av.startRes))
+                .adjustForHiddenColumns(av.getRanges().getStartRes()))
         {
           if (!ap.scrollRight(false))
           {
@@ -404,7 +406,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
         }
         while (seqCanvas.cursorX > av.getColumnSelection()
-                .adjustForHiddenColumns(av.endRes))
+                .adjustForHiddenColumns(av.getRanges().getEndRes()))
         {
           if (!ap.scrollRight(true))
           {
@@ -1772,9 +1774,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       changeStartRes = true;
     }
 
-    if (res < av.getStartRes())
+    if (res < av.getRanges().getStartRes())
     {
-      res = av.getStartRes();
+      res = av.getRanges().getStartRes();
     }
 
     if (changeEndRes)
@@ -1908,13 +1910,15 @@ public class SeqPanel extends JPanel implements MouseListener,
       {
         if (evt != null)
         {
-          if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0))
+          if (mouseDragging && (evt.getY() < 0)
+                  && (av.getRanges().getStartSeq() > 0))
           {
             running = ap.scrollUp(true);
           }
 
           if (mouseDragging && (evt.getY() >= getHeight())
-                  && (av.getAlignment().getHeight() > av.getEndSeq()))
+                  && (av.getAlignment().getHeight() > av.getRanges()
+                          .getEndSeq()))
           {
             running = ap.scrollUp(false);
           }
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 95c3261..1c0420d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -20,10 +20,10 @@
  */
 package jalview.gui;
 
-import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShaderI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.util.Comparison;
 
 import java.awt.Color;
@@ -53,14 +53,13 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   boolean forOverview = false;
 
   /**
-   * Creates a new SequenceRenderer object.
+   * Creates a new SequenceRenderer object
    * 
-   * @param av
-   *          DOCUMENT ME!
+   * @param viewport
    */
-  public SequenceRenderer(AlignViewport av)
+  public SequenceRenderer(AlignViewport viewport)
   {
-    this.av = av;
+    this.av = viewport;
   }
 
   /**
@@ -83,8 +82,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     this.renderGaps = renderGaps;
   }
 
-  @Override
-  public Color getResidueBoxColour(SequenceI seq, int i)
+  protected Color getResidueBoxColour(SequenceI seq, int i)
   {
     // rate limiting step when rendering overview for lots of groups
     allGroups = av.getAlignment().findAllGroups(seq);
@@ -111,20 +109,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    * 
    * @param seq
    * @param position
-   * @param fr
+   * @param finder
    * @return
    */
   @Override
   public Color getResidueColour(final SequenceI seq, int position,
-          FeatureRenderer fr)
+          FeatureColourFinder finder)
   {
-    // TODO replace 8 or so code duplications with calls to this method
-    // (refactored as needed)
     Color col = getResidueBoxColour(seq, position);
 
-    if (fr != null)
+    if (finder != null)
     {
-      col = fr.findFeatureColour(col, seq, position);
+      col = finder.findFeatureColour(col, seq, position);
     }
     return col;
   }
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 34ad659..d7f7c31 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -110,6 +110,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected boolean allChainsSelected = false;
 
+  protected JMenu viewSelectionMenu;
+
   /**
    * Default constructor
    */
@@ -744,17 +746,17 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void itemStateChanged(ItemEvent e)
       {
-        alignStructs.setEnabled(_alignwith.size() > 0);
+        alignStructs.setEnabled(!_alignwith.isEmpty());
         alignStructs.setToolTipText(MessageManager.formatMessage(
                 "label.align_structures_using_linked_alignment_views",
-                new String[] { String.valueOf(_alignwith.size()) }));
+                _alignwith.size()));
       }
     };
-    JMenu alpanels = new ViewSelectionMenu(
+    viewSelectionMenu = new ViewSelectionMenu(
             MessageManager.getString("label.superpose_with"), this,
             _alignwith, handler);
     handler.itemStateChanged(null);
-    viewerActionMenu.add(alpanels);
+    viewerActionMenu.add(viewSelectionMenu, 0);
     viewerActionMenu.addMenuListener(new MenuListener()
     {
       @Override
@@ -781,16 +783,24 @@ public abstract class StructureViewerBase extends GStructureViewer
   public void setJalviewColourScheme(ColourSchemeI cs) {
     getBinding().setJalviewColourScheme(cs);
   }
+
+  /**
+   * Sends commands to the structure viewer to superimpose structures based on
+   * currently associated alignments. May optionally return an error message for
+   * the operation.
+   */
   @Override
-  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+  protected String alignStructs_actionPerformed(
+          ActionEvent actionEvent)
   {
-    alignStructs_withAllAlignPanels();
+    return alignStructs_withAllAlignPanels();
   }
-  protected void alignStructs_withAllAlignPanels()
+
+  protected String alignStructs_withAllAlignPanels()
   {
     if (getAlignmentPanel() == null)
     {
-      return;
+      return null;
     }
   
     if (_alignwith.size() == 0)
@@ -798,6 +808,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       _alignwith.add(getAlignmentPanel());
     }
   
+    String reply = null;
     try
     {
       AlignmentI[] als = new Alignment[_alignwith.size()];
@@ -811,7 +822,13 @@ public abstract class StructureViewerBase extends GStructureViewer
         alm[a] = -1;
         alc[a++] = ap.av.getColumnSelection();
       }
-      getBinding().superposeStructures(als, alm, alc);
+      reply = getBinding().superposeStructures(als, alm, alc);
+      if (reply != null)
+      {
+        String text = MessageManager.formatMessage(
+                "error.superposition_failed", reply);
+        statusBar.setText(text);
+      }
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
@@ -822,7 +839,9 @@ public abstract class StructureViewerBase extends GStructureViewer
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
     }
+    return reply;
   }
+
   @Override
   public void background_actionPerformed(ActionEvent actionEvent)
   {
@@ -952,6 +971,10 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   protected abstract String getViewerName();
+
+  /**
+   * Configures the title and menu items of the viewer panel.
+   */
   public void updateTitleAndMenus()
   {
     AAStructureBindingModel binding = getBinding();
@@ -963,10 +986,30 @@ public abstract class StructureViewerBase extends GStructureViewer
     setChainMenuItems(binding.getChainNames());
   
     this.setTitle(binding.getViewerTitle(getViewerName(), true));
-    if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1)
+
+    /*
+     * enable 'Superpose with' if more than one mapped structure
+     */
+    viewSelectionMenu.setEnabled(false);
+    if (getBinding().getPdbFile().length > 1
+            && getBinding().getSequence().length > 1)
     {
-      viewerActionMenu.setVisible(true);
+      viewSelectionMenu.setEnabled(true);
     }
+
+    /*
+     * Show action menu if it has any enabled items
+     */
+    viewerActionMenu.setVisible(false);
+    for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
+    {
+      if (viewerActionMenu.getItem(i).isEnabled())
+      {
+        viewerActionMenu.setVisible(true);
+        break;
+      }
+    }
+
     if (!binding.isLoadingFromArchive())
     {
       seqColour_actionPerformed(null);
diff --git a/src/jalview/gui/TextColourChooser.java b/src/jalview/gui/TextColourChooser.java
index 49fdaf7..91e05c6 100644
--- a/src/jalview/gui/TextColourChooser.java
+++ b/src/jalview/gui/TextColourChooser.java
@@ -28,11 +28,12 @@ import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
 
 import javax.swing.BorderFactory;
 import javax.swing.JColorChooser;
 import javax.swing.JLabel;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSlider;
 import javax.swing.event.ChangeEvent;
@@ -44,36 +45,43 @@ public class TextColourChooser
 
   SequenceGroup sg;
 
-  public void chooseColour(AlignmentPanel ap, SequenceGroup sg)
+  Color original1, original2;
+
+  int originalThreshold;
+
+  Map<SequenceGroup, Color> groupColour1;
+
+  Map<SequenceGroup, Color> groupColour2;
+
+  Map<SequenceGroup, Integer> groupThreshold;
+
+  /**
+   * Show a dialogue which allows the user to select two text colours and adjust
+   * a slider for the cross-over point
+   * 
+   * @param alignPanel
+   *          the AlignmentPanel context
+   * @param sequenceGroup
+   *          the SequenceGroup context (only for group pop-menu option)
+   */
+  public void chooseColour(AlignmentPanel alignPanel, SequenceGroup sequenceGroup)
   {
-    this.ap = ap;
-    this.sg = sg;
+    this.ap = alignPanel;
+    this.sg = sequenceGroup;
 
-    int original1, original2, originalThreshold;
-    if (sg == null)
-    {
-      original1 = ap.av.getTextColour().getRGB();
-      original2 = ap.av.getTextColour2().getRGB();
-      originalThreshold = ap.av.getThresholdTextColour();
-    }
-    else
-    {
-      original1 = sg.textColour.getRGB();
-      original2 = sg.textColour2.getRGB();
-      originalThreshold = sg.thresholdTextColour;
-    }
+    saveInitialSettings();
 
     final JSlider slider = new JSlider(0, 750, originalThreshold);
     final JPanel col1 = new JPanel();
     col1.setPreferredSize(new Dimension(40, 20));
     col1.setBorder(BorderFactory.createEtchedBorder());
     col1.setToolTipText(MessageManager.getString("label.dark_colour"));
-    col1.setBackground(new Color(original1));
+    col1.setBackground(original1);
     final JPanel col2 = new JPanel();
     col2.setPreferredSize(new Dimension(40, 20));
     col2.setBorder(BorderFactory.createEtchedBorder());
     col2.setToolTipText(MessageManager.getString("label.light_colour"));
-    col2.setBackground(new Color(original2));
+    col2.setBackground(original2);
     final JPanel bigpanel = new JPanel(new BorderLayout());
     JPanel panel = new JPanel();
     bigpanel.add(panel, BorderLayout.CENTER);
@@ -130,7 +138,7 @@ public class TextColourChooser
 
     int reply = JvOptionPane
             .showInternalOptionDialog(
-                    ap,
+                    alignPanel,
                     bigpanel,
                     MessageManager
                             .getString("label.adjunst_foreground_text_colour_threshold"),
@@ -139,19 +147,81 @@ public class TextColourChooser
 
     if (reply == JvOptionPane.CANCEL_OPTION)
     {
-      if (sg == null)
-      {
-        ap.av.setTextColour(new Color(original1));
-        ap.av.setTextColour2(new Color(original2));
-        ap.av.setThresholdTextColour(originalThreshold);
-      }
-      else
+      restoreInitialSettings();
+    }
+  }
+
+  /**
+   * Restore initial settings on Cancel
+   */
+  protected void restoreInitialSettings()
+  {
+    if (sg == null)
+    {
+      ap.av.setTextColour(original1);
+      ap.av.setTextColour2(original2);
+      ap.av.setThresholdTextColour(originalThreshold);
+    }
+    else
+    {
+      sg.textColour = original1;
+      sg.textColour2 = original2;
+      sg.thresholdTextColour = originalThreshold;
+    }
+
+    /*
+     * if 'Apply To All Groups' was in force, there will be 
+     * group-specific settings to restore as well
+     */
+    for (SequenceGroup group : this.groupColour1.keySet())
+    {
+      group.textColour = groupColour1.get(group);
+      group.textColour2 = groupColour2.get(group);
+      group.thresholdTextColour = groupThreshold.get(group);
+    }
+  }
+
+  /**
+   * Save settings on entry, for restore on Cancel
+   */
+  protected void saveInitialSettings()
+  {
+    groupColour1 = new HashMap<SequenceGroup, Color>();
+    groupColour2 = new HashMap<SequenceGroup, Color>();
+    groupThreshold = new HashMap<SequenceGroup, Integer>();
+
+    if (sg == null)
+    {
+      /*
+       * alignment scope
+       */
+      original1 = ap.av.getTextColour();
+      original2 = ap.av.getTextColour2();
+      originalThreshold = ap.av.getThresholdTextColour();
+      if (ap.av.getColourAppliesToAllGroups()
+              && ap.av.getAlignment().getGroups() != null)
       {
-        sg.textColour = new Color(original1);
-        sg.textColour2 = new Color(original2);
-        sg.thresholdTextColour = originalThreshold;
+        /*
+         * if applying changes to all groups, need to be able to 
+         * restore group settings as well
+         */
+        for (SequenceGroup group : ap.av.getAlignment().getGroups())
+        {
+          groupColour1.put(group, group.textColour);
+          groupColour2.put(group, group.textColour2);
+          groupThreshold.put(group, group.thresholdTextColour);
+        }
       }
     }
+    else
+    {
+      /*
+       * Sequence group scope
+       */
+      original1 = sg.textColour;
+      original2 = sg.textColour2;
+      originalThreshold = sg.thresholdTextColour;
+    }
   }
 
   void colour1Changed(Color col)
@@ -215,11 +285,11 @@ public class TextColourChooser
       return;
     }
 
-    for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+    for (SequenceGroup group : ap.av.getAlignment().getGroups())
     {
-      sg.textColour = ap.av.getTextColour();
-      sg.textColour2 = ap.av.getTextColour2();
-      sg.thresholdTextColour = ap.av.getThresholdTextColour();
+      group.textColour = ap.av.getTextColour();
+      group.textColour2 = ap.av.getTextColour2();
+      group.thresholdTextColour = ap.av.getThresholdTextColour();
     }
   }
 
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 54eed1a..9a38d4c 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -549,7 +549,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   public void run()
   {
     PrinterJob printJob = PrinterJob.getPrinterJob();
-    PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+    PageFormat defaultPage = printJob.defaultPage();
+    PageFormat pf = printJob.pageDialog(defaultPage);
+
+    if (defaultPage == pf)
+    {
+      /*
+       * user cancelled
+       */
+      return;
+    }
 
     printJob.setPrintable(this, pf);
 
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 83a8d24..9ab4327 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -29,6 +29,7 @@ import jalview.jbgui.GUserDefinedColours;
 import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
@@ -71,7 +72,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
 
-  private static final int MY_FRAME_HEIGHT = 420;
+  private static final int MY_FRAME_HEIGHT = 440;
 
   private static final int MY_FRAME_WIDTH = 810;
 
@@ -276,14 +277,9 @@ public class UserDefinedColours extends GUserDefinedColours implements
   {
     JButton button = null;
     final Color newColour = colorChooser.getColor();
-    for (int i = 0; i < selectedButtons.size(); i++)
-    {
-      button = selectedButtons.get(i);
-      button.setBackground(newColour);
-      button.setForeground(ColorUtils.brighterThan(newColour));
-    }
     if (lcaseColour.isSelected())
     {
+      selectedButtons.clear();
       for (int i = 0; i < lowerCaseButtons.size(); i++)
       {
         button = lowerCaseButtons.get(i);
@@ -291,6 +287,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
         button.setForeground(ColorUtils.brighterThan(button.getBackground()));
       }
     }
+    for (int i = 0; i < selectedButtons.size(); i++)
+    {
+      button = selectedButtons.get(i);
+      button.setBackground(newColour);
+      button.setForeground(ColorUtils.brighterThan(newColour));
+    }
   }
 
   /**
@@ -589,11 +591,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    // if (ap != null)
-    // {
-    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    // }
-
     return ucs;
   }
 
@@ -625,7 +622,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     File choice = chooser.getSelectedFile();
     Cache.setProperty(LAST_DIRECTORY, choice.getParent());
 
-    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+    UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
             .getAbsolutePath());
     Color[] colors = ucs.getColours();
     schemeName.setText(ucs.getSchemeName());
@@ -674,7 +671,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         colours = colours.substring(0, colours.indexOf("|"));
       }
-      ret = ColourSchemes.loadColourScheme(colours);
+      ret = ColourSchemeLoader.loadColourScheme(colours);
     }
 
     if (ret == null)
diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 27ebe5a..053a65e 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -46,6 +46,7 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
 import jalview.json.binding.biojson.v1.SequencePojo;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.ColorUtils;
@@ -328,6 +329,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       return sequenceFeaturesPojo;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     for (SequenceI seq : sqs)
     {
       SequenceI dataSetSequence = seq.getDatasetSequence();
@@ -350,7 +353,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                   String.valueOf(seq.hashCode()));
 
           String featureColour = (fr == null) ? null : jalview.util.Format
-                  .getHexString(fr.findFeatureColour(Color.white, seq,
+                  .getHexString(finder.findFeatureColour(Color.white, seq,
                           seq.findIndex(sf.getBegin())));
           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
index 746c4a7..0f2b0ac 100644
--- a/src/jalview/io/PDBFeatureSettings.java
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -26,12 +26,14 @@ import jalview.schemes.FeatureSettingsAdapter;
 
 import java.awt.Color;
 
+import MCview.PDBChain;
+
 public class PDBFeatureSettings extends FeatureSettingsAdapter
 {
   // TODO find one central place to define feature names
   private static final String FEATURE_INSERTION = "INSERTION";
 
-  private static final String FEATURE_RES_NUM = "RESNUM";
+  private static final String FEATURE_RES_NUM = PDBChain.RESNUM_FEATURE;
 
   @Override
   public boolean isFeatureDisplayed(String type)
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 4f833bc..7580222 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -221,8 +221,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       ArrayList<String[]> ccomands = new ArrayList<String[]>();
       ArrayList<String> pdbfn = new ArrayList<String>();
       StructureMappingcommandSet[] colcommands = JmolCommands
-              .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
-                      ((AlignmentViewPanel) source).getAlignment());
+              .getColourBySequenceCommand(ssm, modelSet, sequence, sr,
+                      (AlignmentViewPanel) source);
       if (colcommands == null)
       {
         return;
@@ -298,6 +298,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
+  @Override
   public void finalize() throws Throwable
   {
     jvlite = null;
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index b39f4a8..b759d64 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -113,7 +113,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu colourMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
+  protected JMenuItem textColour;
 
   protected JCheckBoxMenuItem conservationMenuItem;
 
@@ -975,7 +975,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem createGroup = new JMenuItem(
-            MessageManager.getString("action.create_groups"));
+            MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1653,6 +1653,7 @@ public class GAlignFrame extends JInternalFrame
 
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -1904,6 +1905,12 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void configureSelectMenu()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
@@ -1921,8 +1928,8 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    textColour = new JRadioButtonMenuItem(
-            MessageManager.getString("action.set_text_colour"));
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 6b89ab4..d8f3f61 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -170,8 +170,8 @@ public abstract class GStructureViewer extends JInternalFrame implements
       }
     });
     alignStructs = new JMenuItem();
-    alignStructs
-            .setText(MessageManager.getString("label.align_structures"));
+    alignStructs.setText(MessageManager
+            .getString("label.superpose_structures"));
     alignStructs.addActionListener(new ActionListener()
     {
       @Override
@@ -181,7 +181,7 @@ public abstract class GStructureViewer extends JInternalFrame implements
       }
     });
 
-    viewerActionMenu = new JMenu();
+    viewerActionMenu = new JMenu(); // text set in sub-classes
     viewerActionMenu.setVisible(false);
     viewerActionMenu.add(alignStructs);
     colourMenu = new JMenu();
@@ -219,9 +219,8 @@ public abstract class GStructureViewer extends JInternalFrame implements
   {
   }
 
-  protected void alignStructs_actionPerformed(ActionEvent actionEvent)
-  {
-  }
+  protected abstract String alignStructs_actionPerformed(
+          ActionEvent actionEvent);
 
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 6f84a2e..3a27c7d 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -307,7 +307,7 @@ public class AnnotationRenderer
   public void updateFromAlignViewport(AlignViewportI av)
   {
     charWidth = av.getCharWidth();
-    endRes = av.getEndRes();
+    endRes = av.getRanges().getEndRes();
     charHeight = av.getCharHeight();
     hasHiddenColumns = av.hasHiddenColumns();
     validCharWidth = av.isValidCharWidth();
diff --git a/src/jalview/renderer/seqfeatures/FeatureColourFinder.java b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
new file mode 100644
index 0000000..1db2004
--- /dev/null
+++ b/src/jalview/renderer/seqfeatures/FeatureColourFinder.java
@@ -0,0 +1,124 @@
+package jalview.renderer.seqfeatures;
+
+import jalview.api.FeatureRenderer;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+
+/**
+ * A helper class to find feature colour using an associated FeatureRenderer
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class FeatureColourFinder
+{
+  /*
+   * the class we delegate feature finding to
+   */
+  private FeatureRenderer featureRenderer;
+
+  /*
+   * a 1-pixel image on which features can be drawn, for the case where
+   * transparency allows 'see-through' of multiple feature colours
+   */
+  private BufferedImage offscreenImage;
+
+  /**
+   * Constructor
+   * 
+   * @param fr
+   */
+  public FeatureColourFinder(FeatureRenderer fr)
+  {
+    featureRenderer = fr;
+    offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
+  }
+
+  /**
+   * Answers the feature colour to show for the given sequence and column
+   * position. This delegates to the FeatureRenderer to find the colour, which
+   * will depend on feature location, visibility, ordering, colour scheme, and
+   * whether or not transparency is applied. For feature rendering with
+   * transparency, this class provides a dummy 'offscreen' graphics context
+   * where multiple feature colours can be overlaid and the combined colour read
+   * back.
+   * <p>
+   * This method is not thread-safe when transparency is applied, since a shared
+   * BufferedImage would be used by all threads to hold the composite colour at
+   * a position. Each thread should use a separate instance of this class.
+   * 
+   * @param defaultColour
+   * @param seq
+   * @param column
+   *          alignment column position (base zero)
+   * @return
+   */
+  public Color findFeatureColour(Color defaultColour, SequenceI seq,
+          int column)
+  {
+    if (noFeaturesDisplayed())
+    {
+      return defaultColour;
+    }
+
+    Graphics g = null;
+
+    /*
+     * if transparency applies, provide a notional 1x1 graphics context 
+     * that has been primed with the default colour
+     */
+    if (featureRenderer.getTransparency() != 1f)
+    {
+      g = offscreenImage.getGraphics();
+      if (defaultColour != null)
+      {
+        offscreenImage.setRGB(0, 0, defaultColour.getRGB());
+      }
+    }
+
+    Color c = featureRenderer.findFeatureColour(seq, column, g);
+    if (c == null)
+    {
+      return defaultColour;
+    }
+
+    if (g != null)
+    {
+      c = new Color(offscreenImage.getRGB(0, 0));
+    }
+    return c;
+  }
+
+  /**
+   * Answers true if feature display is turned off, or there are no features
+   * configured to be visible
+   * 
+   * @return
+   */
+  boolean noFeaturesDisplayed()
+  {
+    if (featureRenderer == null
+            || !featureRenderer.getViewport().isShowSequenceFeatures())
+    {
+      return true;
+    }
+
+    if (!((FeatureRendererModel) featureRenderer).hasRenderOrder())
+    {
+      return true;
+    }
+
+    FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed();
+    if (displayed == null || displayed.getVisibleFeatureCount() == 0)
+    {
+      return true;
+    }
+
+    return false;
+  }
+}
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 9e0089f..72ac2c8 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -23,6 +23,7 @@ package jalview.renderer.seqfeatures;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.AlphaComposite;
@@ -30,28 +31,11 @@ import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
 
 public class FeatureRenderer extends FeatureRendererModel
 {
-
-  FontMetrics fm;
-
-  int charOffset;
-
-  boolean offscreenRender = false;
-
-  protected SequenceI lastSeq;
-
-  char s;
-
-  int i;
-
-  int av_charHeight, av_charWidth;
-
-  boolean av_validCharWidth, av_isShowSeqFeatureHeight;
-
-  private Integer currentColour;
+  private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
+          .getInstance(AlphaComposite.SRC_OVER, 1.0f);
 
   /**
    * Constructor given a viewport
@@ -63,273 +47,252 @@ public class FeatureRenderer extends FeatureRendererModel
     this.av = viewport;
   }
 
-  protected void updateAvConfig()
+  /**
+   * Renders the sequence using the given feature colour between the given start
+   * and end columns. Returns true if at least one column is drawn, else false
+   * (the feature range does not overlap the start and end positions).
+   * 
+   * @param g
+   * @param seq
+   * @param featureStart
+   * @param featureEnd
+   * @param featureColour
+   * @param start
+   * @param end
+   * @param y1
+   * @param colourOnly
+   * @return
+   */
+  boolean renderFeature(Graphics g, SequenceI seq, int featureStart,
+          int featureEnd, Color featureColour, int start, int end, int y1,
+          boolean colourOnly)
   {
-    av_charHeight = av.getCharHeight();
-    av_charWidth = av.getCharWidth();
-    av_validCharWidth = av.isValidCharWidth();
-    av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight();
-  }
+    int charHeight = av.getCharHeight();
+    int charWidth = av.getCharWidth();
+    boolean validCharWidth = av.isValidCharWidth();
 
-  void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
-          Color featureColour, int start, int end, int y1)
-  {
-    updateAvConfig();
-    if (((fstart <= end) && (fend >= start)))
+    if (featureStart > end || featureEnd < start)
     {
-      if (fstart < start)
-      { // fix for if the feature we have starts before the sequence start,
-        fstart = start; // but the feature end is still valid!!
-      }
-
-      if (fend >= end)
-      {
-        fend = end;
-      }
-      int pady = (y1 + av_charHeight) - av_charHeight / 5;
-      for (i = fstart; i <= fend; i++)
-      {
-        s = seq.getCharAt(i);
-
-        if (jalview.util.Comparison.isGap(s))
-        {
-          continue;
-        }
-
-        g.setColor(featureColour);
-
-        g.fillRect((i - start) * av_charWidth, y1, av_charWidth,
-                av_charHeight);
-
-        if (offscreenRender || !av_validCharWidth)
-        {
-          continue;
-        }
-
-        g.setColor(Color.white);
-        charOffset = (av_charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s), charOffset
-                + (av_charWidth * (i - start)), pady);
+      return false;
+    }
 
-      }
+    if (featureStart < start)
+    {
+      featureStart = start;
     }
-  }
+    if (featureEnd >= end)
+    {
+      featureEnd = end;
+    }
+    int pady = (y1 + charHeight) - charHeight / 5;
 
-  void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
-          Color featureColour, int start, int end, int y1, byte[] bs)
-  {
-    updateAvConfig();
-    if (((fstart <= end) && (fend >= start)))
+    FontMetrics fm = g.getFontMetrics();
+    for (int i = featureStart; i <= featureEnd; i++)
     {
-      if (fstart < start)
-      { // fix for if the feature we have starts before the sequence start,
-        fstart = start; // but the feature end is still valid!!
-      }
+      char s = seq.getCharAt(i);
 
-      if (fend >= end)
-      {
-        fend = end;
-      }
-      int pady = (y1 + av_charHeight) - av_charHeight / 5;
-      int ystrt = 0, yend = av_charHeight;
-      if (bs[0] != 0)
-      {
-        // signed - zero is always middle of residue line.
-        if (bs[1] < 128)
-        {
-          yend = av_charHeight * (128 - bs[1]) / 512;
-          ystrt = av_charHeight - yend / 2;
-        }
-        else
-        {
-          ystrt = av_charHeight / 2;
-          yend = av_charHeight * (bs[1] - 128) / 512;
-        }
-      }
-      else
+      if (Comparison.isGap(s))
       {
-        yend = av_charHeight * bs[1] / 255;
-        ystrt = av_charHeight - yend;
-
+        continue;
       }
-      for (i = fstart; i <= fend; i++)
-      {
-        s = seq.getCharAt(i);
-
-        if (jalview.util.Comparison.isGap(s))
-        {
-          continue;
-        }
 
-        g.setColor(featureColour);
-        int x = (i - start) * av_charWidth;
-        g.drawRect(x, y1, av_charWidth, av_charHeight);
-        g.fillRect(x, y1 + ystrt, av_charWidth, yend);
+      g.setColor(featureColour);
 
-        if (offscreenRender || !av_validCharWidth)
-        {
-          continue;
-        }
+      g.fillRect((i - start) * charWidth, y1, charWidth,
+              charHeight);
 
-        g.setColor(Color.black);
-        charOffset = (av_charWidth - fm.charWidth(s)) / 2;
-        g.drawString(String.valueOf(s), charOffset
-                + (av_charWidth * (i - start)), pady);
+      if (colourOnly || !validCharWidth)
+      {
+        continue;
       }
-    }
-  }
-
-  BufferedImage offscreenImage;
 
-  @Override
-  public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
-  {
-    return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
+      g.setColor(Color.white);
+      int charOffset = (charWidth - fm.charWidth(s)) / 2;
+      g.drawString(String.valueOf(s), charOffset
+              + (charWidth * (i - start)), pady);
+    }
+    return true;
   }
 
   /**
-   * This is used by Structure Viewers and the Overview Window to get the
-   * feature colour of the rendered sequence, returned as an RGB value
+   * Renders the sequence using the given SCORE feature colour between the given
+   * start and end columns. Returns true if at least one column is drawn, else
+   * false (the feature range does not overlap the start and end positions).
    * 
-   * @param defaultColour
+   * @param g
    * @param seq
-   * @param column
+   * @param fstart
+   * @param fend
+   * @param featureColour
+   * @param start
+   * @param end
+   * @param y1
+   * @param bs
+   * @param colourOnly
    * @return
    */
-  public synchronized int findFeatureColour(int defaultColour,
-          final SequenceI seq, int column)
+  boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,
+          int fend, Color featureColour, int start, int end, int y1,
+          byte[] bs, boolean colourOnly)
   {
-    if (!av.isShowSequenceFeatures())
+    if (fstart > end || fend < start)
     {
-      return defaultColour;
+      return false;
     }
 
-    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
-    if (seq != lastSeq)
+    if (fstart < start)
+    { // fix for if the feature we have starts before the sequence start,
+      fstart = start; // but the feature end is still valid!!
+    }
+
+    if (fend >= end)
+    {
+      fend = end;
+    }
+    int charHeight = av.getCharHeight();
+    int pady = (y1 + charHeight) - charHeight / 5;
+    int ystrt = 0, yend = charHeight;
+    if (bs[0] != 0)
     {
-      lastSeq = seq;
-      lastSequenceFeatures = sequenceFeatures;
-      if (lastSequenceFeatures != null)
+      // signed - zero is always middle of residue line.
+      if (bs[1] < 128)
       {
-        sfSize = lastSequenceFeatures.length;
+        yend = charHeight * (128 - bs[1]) / 512;
+        ystrt = charHeight - yend / 2;
+      }
+      else
+      {
+        ystrt = charHeight / 2;
+        yend = charHeight * (bs[1] - 128) / 512;
       }
     }
     else
     {
-      if (lastSequenceFeatures != sequenceFeatures)
+      yend = charHeight * bs[1] / 255;
+      ystrt = charHeight - yend;
+
+    }
+
+    FontMetrics fm = g.getFontMetrics();
+    int charWidth = av.getCharWidth();
+
+    for (int i = fstart; i <= fend; i++)
+    {
+      char s = seq.getCharAt(i);
+
+      if (Comparison.isGap(s))
       {
-        lastSequenceFeatures = sequenceFeatures;
-        if (lastSequenceFeatures != null)
-        {
-          sfSize = lastSequenceFeatures.length;
-        }
+        continue;
       }
+
+      g.setColor(featureColour);
+      int x = (i - start) * charWidth;
+      g.drawRect(x, y1, charWidth, charHeight);
+      g.fillRect(x, y1 + ystrt, charWidth, yend);
+
+      if (colourOnly || !av.isValidCharWidth())
+      {
+        continue;
+      }
+
+      g.setColor(Color.black);
+      int charOffset = (charWidth - fm.charWidth(s)) / 2;
+      g.drawString(String.valueOf(s), charOffset
+              + (charWidth * (i - start)), pady);
     }
+    return true;
+  }
 
-    if (lastSequenceFeatures == null || sfSize == 0)
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Color findFeatureColour(SequenceI seq, int column, Graphics g)
+  {
+    if (!av.isShowSequenceFeatures())
     {
-      return defaultColour;
+      return null;
     }
 
-    if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
+    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
+
+    if (sequenceFeatures == null || sequenceFeatures.length == 0)
     {
-      return Color.white.getRGB();
+      return null;
     }
 
-    // Only bother making an offscreen image if transparency is applied
-    if (transparency != 1.0f && offscreenImage == null)
+    if (Comparison.isGap(seq.getCharAt(column)))
     {
-      offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
+      return Color.white;
     }
 
-    currentColour = null;
-    // TODO: non-threadsafe - each rendering thread needs its own instance of
-    // the feature renderer - or this should be synchronized.
-    offscreenRender = true;
-
-    if (offscreenImage != null)
+    Color renderedColour = null;
+    if (transparency == 1.0f)
     {
-      offscreenImage.setRGB(0, 0, defaultColour);
-      drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
-
-      return offscreenImage.getRGB(0, 0);
+      /*
+       * simple case - just find the topmost rendered visible feature colour
+       */
+      renderedColour = findFeatureColour(seq, seq.findPosition(column));
     }
     else
     {
-      drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
-
-      if (currentColour == null)
-      {
-        return defaultColour;
-      }
-      else
-      {
-        return currentColour.intValue();
-      }
+      /*
+       * transparency case - draw all visible features in render order to
+       * build up a composite colour on the graphics context
+       */
+      renderedColour = drawSequence(g, seq, column, column, 0, true);
     }
-
+    return renderedColour;
   }
 
-  private volatile SequenceFeature[] lastSequenceFeatures;
-
-  int sfSize;
-
-  int sfindex;
-
-  int spos;
-
-  int epos;
-
   /**
-   * Draws the sequence on the graphics context, or just determines the colour
-   * that would be drawn (if flag offscreenrender is true).
+   * Draws the sequence features on the graphics context, or just determines the
+   * colour that would be drawn (if flag colourOnly is true). Returns the last
+   * colour drawn (which may not be the effective colour if transparency
+   * applies), or null if no feature is drawn in the range given.
    * 
    * @param g
+   *          the graphics context to draw on (may be null if colourOnly==true)
    * @param seq
    * @param start
-   *          start column (or sequence position in offscreenrender mode)
+   *          start column
    * @param end
-   *          end column (not used in offscreenrender mode)
+   *          end column
    * @param y1
    *          vertical offset at which to draw on the graphics
+   * @param colourOnly
+   *          if true, only do enough to determine the colour for the position,
+   *          do not draw the character
+   * @return
    */
-  public synchronized void drawSequence(Graphics g, final SequenceI seq,
-          int start, int end, int y1)
+  public synchronized Color drawSequence(final Graphics g,
+          final SequenceI seq, int start, int end, int y1,
+          boolean colourOnly)
   {
     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
     if (sequenceFeatures == null || sequenceFeatures.length == 0)
     {
-      return;
-    }
-
-    if (g != null)
-    {
-      fm = g.getFontMetrics();
+      return null;
     }
 
     updateFeatures();
 
-    if (lastSeq == null || seq != lastSeq
-            || sequenceFeatures != lastSequenceFeatures)
-    {
-      lastSeq = seq;
-      lastSequenceFeatures = sequenceFeatures;
-    }
-
-    if (transparency != 1 && g != null)
+    if (transparency != 1f && g != null)
     {
       Graphics2D g2 = (Graphics2D) g;
       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
               transparency));
     }
 
-    if (!offscreenRender)
-    {
-      spos = lastSeq.findPosition(start);
-      epos = lastSeq.findPosition(end);
-    }
+    int startPos = seq.findPosition(start);
+    int endPos = seq.findPosition(end);
+
+    int sfSize = sequenceFeatures.length;
+    Color drawnColour = null;
 
-    sfSize = lastSequenceFeatures.length;
+    /*
+     * iterate over features in ordering of their rendering (last is on top)
+     */
     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
     {
       String type = renderOrder[renderIndex];
@@ -340,27 +303,29 @@ public class FeatureRenderer extends FeatureRendererModel
 
       // loop through all features in sequence to find
       // current feature to render
-      for (sfindex = 0; sfindex < sfSize; sfindex++)
+      for (int sfindex = 0; sfindex < sfSize; sfindex++)
       {
-        final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
+        final SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
         if (!sequenceFeature.type.equals(type))
         {
           continue;
         }
 
+        /*
+         * a feature type may be flagged as shown but the group 
+         * an instance of it belongs to may be hidden
+         */
         if (featureGroupNotShown(sequenceFeature))
         {
           continue;
         }
 
         /*
-         * check feature overlaps the visible part of the alignment, 
-         * unless doing offscreenRender (to the Overview window or a 
-         * structure viewer) which is not limited 
+         * check feature overlaps the target range
+         * TODO: efficient retrieval of features overlapping a range
          */
-        if (!offscreenRender
-                && (sequenceFeature.getBegin() > epos || sequenceFeature
-                        .getEnd() < spos))
+        if (sequenceFeature.getBegin() > endPos
+                || sequenceFeature.getEnd() < startPos)
         {
           continue;
         }
@@ -368,58 +333,46 @@ public class FeatureRenderer extends FeatureRendererModel
         Color featureColour = getColour(sequenceFeature);
         boolean isContactFeature = sequenceFeature.isContactFeature();
 
-        if (offscreenRender && offscreenImage == null)
-        {
-          /*
-           * offscreen mode with no image (image is only needed if transparency 
-           * is applied to feature colours) - just check feature is rendered at 
-           * the requested position (start == sequence position in this mode)
-           */
-          boolean featureIsAtPosition = sequenceFeature.begin <= start
-                  && sequenceFeature.end >= start;
-          if (isContactFeature)
-          {
-            featureIsAtPosition = sequenceFeature.begin == start
-                    || sequenceFeature.end == start;
-          }
-          if (featureIsAtPosition)
-          {
-            // this is passed out to the overview and other sequence renderers
-            // (e.g. molecule viewer) to get displayed colour for rendered
-            // sequence
-            currentColour = new Integer(featureColour.getRGB());
-            // used to be retreived from av.featuresDisplayed
-            // currentColour = av.featuresDisplayed
-            // .get(sequenceFeatures[sfindex].type);
-
-          }
-        }
-        else if (isContactFeature)
+        if (isContactFeature)
         {
-          renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
+          boolean drawn = renderFeature(g, seq,
+                  seq.findIndex(sequenceFeature.begin) - 1,
                   seq.findIndex(sequenceFeature.begin) - 1, featureColour,
-                  start, end, y1);
-          renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
+                  start, end, y1, colourOnly);
+          drawn |= renderFeature(g, seq,
+                  seq.findIndex(sequenceFeature.end) - 1,
                   seq.findIndex(sequenceFeature.end) - 1, featureColour,
-                  start, end, y1);
-
+                  start, end, y1, colourOnly);
+          if (drawn)
+          {
+            drawnColour = featureColour;
+          }
         }
         else if (showFeature(sequenceFeature))
         {
-          if (av_isShowSeqFeatureHeight
+          if (av.isShowSequenceFeaturesHeight()
                   && !Float.isNaN(sequenceFeature.score))
           {
-            renderScoreFeature(g, seq,
+            boolean drawn = renderScoreFeature(g, seq,
                     seq.findIndex(sequenceFeature.begin) - 1,
-                    seq.findIndex(sequenceFeature.end) - 1,
-                    featureColour, start, end, y1,
-                    normaliseScore(sequenceFeature));
+                    seq.findIndex(sequenceFeature.end) - 1, featureColour,
+                    start, end, y1, normaliseScore(sequenceFeature),
+                    colourOnly);
+            if (drawn)
+            {
+              drawnColour = featureColour;
+            }
           }
           else
           {
-            renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
-                    seq.findIndex(sequenceFeature.end) - 1,
-                    featureColour, start, end, y1);
+            boolean drawn = renderFeature(g, seq,
+                    seq.findIndex(sequenceFeature.begin) - 1,
+                    seq.findIndex(sequenceFeature.end) - 1, featureColour,
+                    start, end, y1, colourOnly);
+            if (drawn)
+            {
+              drawnColour = featureColour;
+            }
           }
         }
       }
@@ -427,10 +380,14 @@ public class FeatureRenderer extends FeatureRendererModel
 
     if (transparency != 1.0f && g != null)
     {
+      /*
+       * reset transparency
+       */
       Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
-              1.0f));
+      g2.setComposite(NO_TRANSPARENCY);
     }
+
+    return drawnColour;
   }
 
   /**
@@ -459,7 +416,78 @@ public class FeatureRenderer extends FeatureRendererModel
   @Override
   public void featuresAdded()
   {
-    lastSeq = null;
     findAllFeatures();
   }
+
+  /**
+   * Returns the sequence feature colour rendered at the given sequence
+   * position, or null if none found. The feature of highest render order (i.e.
+   * on top) is found, subject to both feature type and feature group being
+   * visible, and its colour returned.
+   * 
+   * @param seq
+   * @param pos
+   * @return
+   */
+  Color findFeatureColour(SequenceI seq, int pos)
+  {
+    SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
+    if (sequenceFeatures == null || sequenceFeatures.length == 0)
+    {
+      return null;
+    }
+  
+    /*
+     * check for new feature added while processing
+     */
+    updateFeatures();
+
+    /*
+     * inspect features in reverse renderOrder (the last in the array is 
+     * displayed on top) until we find one that is rendered at the position
+     */
+    for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
+    {
+      String type = renderOrder[renderIndex];
+      if (!showFeatureOfType(type))
+      {
+        continue;
+      }
+
+      for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
+      {
+        SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
+        if (!sequenceFeature.type.equals(type))
+        {
+          continue;
+        }
+
+        if (featureGroupNotShown(sequenceFeature))
+        {
+          continue;
+        }
+
+        /*
+         * check the column position is within the feature range
+         * (or is one of the two contact positions for a contact feature)
+         */
+        boolean featureIsAtPosition = sequenceFeature.begin <= pos
+                && sequenceFeature.end >= pos;
+        if (sequenceFeature.isContactFeature())
+        {
+          featureIsAtPosition = sequenceFeature.begin == pos
+                  || sequenceFeature.end == pos;
+        }
+        if (featureIsAtPosition)
+        {
+          return getColour(sequenceFeature);
+        }
+      }
+    }
+  
+    /*
+     * no displayed feature found at position
+     */
+    return null;
+  }
 }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 1a3e9ef..220d3ab 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -27,6 +27,8 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.AnnotationRenderer;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.IdentityHashMap;
@@ -40,15 +42,25 @@ public class AnnotationColourGradient extends FollowerColourScheme
 
   public static final int ABOVE_THRESHOLD = 1;
 
-  public AlignmentAnnotation annotation;
+  private final AlignmentAnnotation annotation;
 
-  int aboveAnnotationThreshold = -1;
+  private final int aboveAnnotationThreshold;
 
   public boolean thresholdIsMinMax = false;
 
-  GraphLine annotationThreshold;
+  private GraphLine annotationThreshold;
 
-  float r1, g1, b1, rr, gg, bb;
+  private int redMin;
+
+  private int greenMin;
+
+  private int blueMin;
+
+  private int redRange;
+
+  private int greenRange;
+
+  private int blueRange;
 
   private boolean predefinedColours = false;
 
@@ -61,7 +73,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
    */
   private boolean noGradient = false;
 
-  IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+  private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
   public ColourSchemeI getInstance(AnnotatedCollectionI sg,
@@ -72,12 +84,12 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.thresholdIsMinMax = thresholdIsMinMax;
     acg.annotationThreshold = (annotationThreshold == null) ? null
             : new GraphLine(annotationThreshold);
-    acg.r1 = r1;
-    acg.g1 = g1;
-    acg.b1 = b1;
-    acg.rr = rr;
-    acg.gg = gg;
-    acg.bb = bb;
+    acg.redMin = redMin;
+    acg.greenMin = greenMin;
+    acg.blueMin = blueMin;
+    acg.redRange = redRange;
+    acg.greenRange = greenRange;
+    acg.blueRange = blueRange;
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
     acg.noGradient = noGradient;
@@ -109,12 +121,12 @@ public class AnnotationColourGradient extends FollowerColourScheme
       annotationThreshold = annotation.threshold;
     }
     // clear values so we don't get weird black bands...
-    r1 = 254;
-    g1 = 254;
-    b1 = 254;
-    rr = 0;
-    gg = 0;
-    bb = 0;
+    redMin = 254;
+    greenMin = 254;
+    blueMin = 254;
+    redRange = 0;
+    greenRange = 0;
+    blueRange = 0;
 
     noGradient = true;
     checkLimits();
@@ -135,13 +147,13 @@ public class AnnotationColourGradient extends FollowerColourScheme
       annotationThreshold = annotation.threshold;
     }
 
-    r1 = minColour.getRed();
-    g1 = minColour.getGreen();
-    b1 = minColour.getBlue();
+    redMin = minColour.getRed();
+    greenMin = minColour.getGreen();
+    blueMin = minColour.getBlue();
 
-    rr = maxColour.getRed() - r1;
-    gg = maxColour.getGreen() - g1;
-    bb = maxColour.getBlue() - b1;
+    redRange = maxColour.getRed() - redMin;
+    greenRange = maxColour.getGreen() - greenMin;
+    blueRange = maxColour.getBlue() - blueMin;
 
     noGradient = false;
     checkLimits();
@@ -211,9 +223,9 @@ public class AnnotationColourGradient extends FollowerColourScheme
 
   float aamin = 0f, aamax = 0f;
 
-  public String getAnnotation()
+  public AlignmentAnnotation getAnnotation()
   {
-    return annotation.label;
+    return annotation;
   }
 
   public int getAboveThreshold()
@@ -235,12 +247,13 @@ public class AnnotationColourGradient extends FollowerColourScheme
 
   public Color getMinColour()
   {
-    return new Color((int) r1, (int) g1, (int) b1);
+    return new Color(redMin, greenMin, blueMin);
   }
 
   public Color getMaxColour()
   {
-    return new Color((int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+    return new Color(redMin + redRange, greenMin + greenRange, blueMin
+            + blueRange);
   }
 
   /**
@@ -258,137 +271,157 @@ public class AnnotationColourGradient extends FollowerColourScheme
   }
 
   /**
-   * DOCUMENT ME!
+   * Returns the colour for a given character and position in a sequence
    * 
-   * @param n
-   *          DOCUMENT ME!
+   * @param c
+   *          the residue character
    * @param j
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   *          the aligned position
+   * @param seq
+   *          the sequence
+   * @return
    */
   @Override
   public Color findColour(char c, int j, SequenceI seq)
   {
-    Color currentColour = Color.white;
-    AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+    /*
+     * locate the annotation we are configured to colour by
+     */
+    AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
             .get(seq) : this.annotation);
-    if (annotation == null)
+
+    /*
+     * if gap or no annotation at position, no colour (White)
+     */
+    if (ann == null || ann.annotations == null
+            || j >= ann.annotations.length || ann.annotations[j] == null
+            || Comparison.isGap(c))
     {
-      return currentColour;
+      return Color.white;
     }
-    // if ((threshold == 0) || aboveThreshold(c, j))
-    // {
-    if (annotation.annotations != null && j < annotation.annotations.length
-            && annotation.annotations[j] != null
-            && !jalview.util.Comparison.isGap(c))
+
+    Annotation aj = ann.annotations[j];
+    // 'use original colours' => colourScheme != null
+    // -> look up colour to be used
+    // predefined colours => preconfigured shading
+    // -> only use original colours reference if thresholding enabled &
+    // minmax exists
+    // annotation.hasIcons => null or black colours replaced with glyph
+    // colours
+    // -> reuse original colours if present
+    // -> if thresholding enabled then return colour on non-whitespace glyph
+
+    /*
+     * if threshold applies, and annotation fails the test - no colour (white)
+     */
+    if (annotationThreshold != null)
     {
-      Annotation aj = annotation.annotations[j];
-      // 'use original colours' => colourScheme != null
-      // -> look up colour to be used
-      // predefined colours => preconfigured shading
-      // -> only use original colours reference if thresholding enabled &
-      // minmax exists
-      // annotation.hasIcons => null or black colours replaced with glyph
-      // colours
-      // -> reuse original colours if present
-      // -> if thresholding enabled then return colour on non-whitespace glyph
-
-      if (aboveAnnotationThreshold == NO_THRESHOLD
-              || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
-                      : aj.value <= annotationThreshold.value)))
+      if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value < annotationThreshold.value)
+              || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
       {
-        if (predefinedColours && aj.colour != null
-                && !aj.colour.equals(Color.black))
-        {
-          currentColour = aj.colour;
-        }
-        else if (annotation.hasIcons
-                && annotation.graph == AlignmentAnnotation.NO_GRAPH)
+        return Color.white;
+      }
+    }
+
+    /*
+     * If 'use original colours' then return the colour of the annotation
+     * at the aligned position - computed using the background colour scheme
+     */
+    if (predefinedColours && aj.colour != null
+            && !aj.colour.equals(Color.black))
+    {
+      return aj.colour;
+    }
+
+    Color result = Color.white;
+    if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH)
+    {
+      /*
+       * secondary structure symbol colouring
+       */
+      if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+              && aj.secondaryStructure != '-')
+      {
+        if (getColourScheme() != null)
         {
-          if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
-                  && aj.secondaryStructure != '-')
-          {
-            if (getColourScheme() != null)
-            {
-              currentColour = getColourScheme().findColour(c, j, seq, null,
-                      0f);
-            }
-            else
-            {
-              if (annotation.isRNA())
-              {
-                currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
-              }
-              else
-              {
-                currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
-                        : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
-                                : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
-              }
-            }
-          }
-          else
-          {
-            //
-            return Color.white;
-          }
+          result = getColourScheme().findColour(c, j, seq, null, 0f);
         }
-        else if (noGradient)
+        else
         {
-          if (getColourScheme() != null)
+          if (ann.isRNA())
           {
-            currentColour = getColourScheme().findColour(c, j, seq, null,
-                    0f);
+            result = ColourSchemeProperty.rnaHelices[(int) aj.value];
           }
           else
           {
-            if (aj.colour != null)
-            {
-              currentColour = aj.colour;
-            }
+            result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
+                    : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+                            : AnnotationRenderer.STEM_COLOUR;
           }
         }
-        else
+      }
+      else
+      {
+        return Color.white;
+      }
+    }
+    else if (noGradient)
+    {
+      if (getColourScheme() != null)
+      {
+        result = getColourScheme().findColour(c, j, seq, null, 0f);
+      }
+      else
+      {
+        if (aj.colour != null)
         {
-          currentColour = shadeCalculation(annotation, j);
+          result = aj.colour;
         }
       }
-      // if (conservationColouring)
-      // {
-      // currentColour = applyConservation(currentColour, j);
-      // }
     }
-    // }
-    return currentColour;
+    else
+    {
+      result = shadeCalculation(ann, j);
+    }
+
+    return result;
   }
 
-  private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+  /**
+   * Returns a graduated colour for the annotation at the given column. If there
+   * is a threshold value, and it is used as the top/bottom of the colour range,
+   * and the value satisfies the threshold condition, then a colour
+   * proportionate to the range from the threshold is calculated. For all other
+   * cases, a colour proportionate to the annotation's min-max range is
+   * calulated. Note that thresholding is _not_ done here (a colour is computed
+   * even if threshold is not passed).
+   * 
+   * @param ann
+   * @param col
+   * @return
+   */
+  Color shadeCalculation(AlignmentAnnotation ann, int col)
   {
-
-    // calculate a shade
     float range = 1f;
-    if (thresholdIsMinMax
-            && annotation.threshold != null
+    float value = ann.annotations[col].value;
+    if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == ABOVE_THRESHOLD
-            && annotation.annotations[j].value >= annotation.threshold.value)
+            && value >= ann.threshold.value)
     {
-      range = (annotation.annotations[j].value - annotation.threshold.value)
-              / (annotation.graphMax - annotation.threshold.value);
+      range = (value - ann.threshold.value)
+              / (ann.graphMax - ann.threshold.value);
     }
-    else if (thresholdIsMinMax && annotation.threshold != null
+    else if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == BELOW_THRESHOLD
-            && annotation.annotations[j].value >= annotation.graphMin)
+            && value <= ann.threshold.value)
     {
-      range = (annotation.annotations[j].value - annotation.graphMin)
-              / (annotation.threshold.value - annotation.graphMin);
+      range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
     }
     else
     {
-      if (annotation.graphMax != annotation.graphMin)
+      if (ann.graphMax != ann.graphMin)
       {
-        range = (annotation.annotations[j].value - annotation.graphMin)
-                / (annotation.graphMax - annotation.graphMin);
+        range = (value - ann.graphMin) / (ann.graphMax - ann.graphMin);
       }
       else
       {
@@ -396,11 +429,11 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
     }
 
-    int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
-            * range + b1);
+    int dr = (int) (redRange * range + redMin);
+    int dg = (int) (greenRange * range + greenMin);
+    int db = (int) (blueRange * range + blueMin);
 
     return new Color(dr, dg, db);
-
   }
 
   public boolean isPredefinedColours()
@@ -423,6 +456,16 @@ public class AnnotationColourGradient extends FollowerColourScheme
     seqAssociated = sassoc;
   }
 
+  public boolean isThresholdIsMinMax()
+  {
+    return thresholdIsMinMax;
+  }
+
+  public void setThresholdIsMinMax(boolean minMax)
+  {
+    this.thresholdIsMinMax = minMax;
+  }
+
   @Override
   public String getSchemeName()
   {
diff --git a/src/jalview/schemes/ColourSchemeLoader.java b/src/jalview/schemes/ColourSchemeLoader.java
new file mode 100644
index 0000000..8660f3e
--- /dev/null
+++ b/src/jalview/schemes/ColourSchemeLoader.java
@@ -0,0 +1,125 @@
+package jalview.schemes;
+
+import jalview.binding.JalviewUserColours;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+public class ColourSchemeLoader
+{
+
+  /**
+   * Loads a user defined colour scheme from file. The file should contain a
+   * definition of residue colours in XML format as defined in
+   * JalviewUserColours.xsd.
+   * 
+   * @param filePath
+   * 
+   * @return
+   */
+  public static UserColourScheme loadColourScheme(String filePath)
+  {
+    UserColourScheme ucs = null;
+    Color[] newColours = null;
+    File file = new File(filePath);
+    try
+    {
+      InputStreamReader in = new InputStreamReader(
+              new FileInputStream(file), "UTF-8");
+  
+      jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
+  
+      org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
+              jucs);
+      jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
+              .unmarshal(in);
+  
+      /*
+       * non-case-sensitive colours are for 20 amino acid codes,
+       * B, Z, X and Gap
+       * optionally, lower-case alternatives for all except Gap
+       */
+      newColours = new Color[24];
+      Color[] lowerCase = new Color[23];
+      boolean caseSensitive = false;
+  
+      String name;
+      int index;
+      for (int i = 0; i < jucs.getColourCount(); i++)
+      {
+        name = jucs.getColour(i).getName();
+        if (ResidueProperties.aa3Hash.containsKey(name))
+        {
+          index = ResidueProperties.aa3Hash.get(name).intValue();
+        }
+        else
+        {
+          index = ResidueProperties.aaIndex[name.charAt(0)];
+        }
+        if (index == -1)
+        {
+          continue;
+        }
+  
+        Color color = new Color(Integer.parseInt(jucs.getColour(i)
+                .getRGB(), 16));
+        if (name.toLowerCase().equals(name))
+        {
+          caseSensitive = true;
+          lowerCase[index] = color;
+        }
+        else
+        {
+          newColours[index] = color;
+        }
+      }
+  
+      /*
+       * instantiate the colour scheme
+       */
+      ucs = new UserColourScheme(newColours);
+      ucs.setName(jucs.getSchemeName());
+      if (caseSensitive)
+      {
+        ucs.setLowerCaseColours(lowerCase);
+      }
+    } catch (Exception ex)
+    {
+      // Could be old Jalview Archive format
+      try
+      {
+        InputStreamReader in = new InputStreamReader(new FileInputStream(
+                file), "UTF-8");
+  
+        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
+  
+        jucs = JalviewUserColours.unmarshal(in);
+  
+        newColours = new Color[jucs.getColourCount()];
+  
+        for (int i = 0; i < 24; i++)
+        {
+          newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
+                  .getRGB(), 16));
+        }
+        ucs = new UserColourScheme(newColours);
+        ucs.setName(jucs.getSchemeName());
+      } catch (Exception ex2)
+      {
+        ex2.printStackTrace();
+      }
+  
+      if (newColours == null)
+      {
+        System.out.println("Error loading User ColourFile\n" + ex);
+      }
+    }
+  
+    return ucs;
+  }
+
+}
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 817fb01..dc7e403 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,14 +1,9 @@
 package jalview.schemes;
 
-import jalview.binding.JalviewUserColours;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
-import java.awt.Color;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
@@ -177,114 +172,4 @@ public class ColourSchemes
     }
     return false;
   }
-
-  /**
-   * Loads a user defined colour scheme from file. The file should contain a
-   * definition of residue colours in XML format as defined in
-   * JalviewUserColours.xsd.
-   * 
-   * @param filePath
-   * 
-   * @return
-   */
-  public static UserColourScheme loadColourScheme(String filePath)
-  {
-    UserColourScheme ucs = null;
-    Color[] newColours = null;
-    File file = new File(filePath);
-    try
-    {
-      InputStreamReader in = new InputStreamReader(
-              new FileInputStream(file), "UTF-8");
-  
-      jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-  
-      org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
-              jucs);
-      jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
-              .unmarshal(in);
-  
-      /*
-       * non-case-sensitive colours are for 20 amino acid codes,
-       * B, Z, X and Gap
-       * optionally, lower-case alternatives for all except Gap
-       */
-      newColours = new Color[24];
-      Color[] lowerCase = new Color[23];
-      boolean caseSensitive = false;
-  
-      String name;
-      int index;
-      for (int i = 0; i < jucs.getColourCount(); i++)
-      {
-        name = jucs.getColour(i).getName();
-        if (ResidueProperties.aa3Hash.containsKey(name))
-        {
-          index = ResidueProperties.aa3Hash.get(name).intValue();
-        }
-        else
-        {
-          index = ResidueProperties.aaIndex[name.charAt(0)];
-        }
-        if (index == -1)
-        {
-          continue;
-        }
-  
-        Color color = new Color(Integer.parseInt(jucs.getColour(i)
-                .getRGB(), 16));
-        if (name.toLowerCase().equals(name))
-        {
-          caseSensitive = true;
-          lowerCase[index] = color;
-        }
-        else
-        {
-          newColours[index] = color;
-        }
-      }
-  
-      /*
-       * instantiate the colour scheme
-       */
-      ucs = new UserColourScheme(newColours);
-      ucs.setName(jucs.getSchemeName());
-      if (caseSensitive)
-      {
-        ucs.setLowerCaseColours(lowerCase);
-      }
-    } catch (Exception ex)
-    {
-      // Could be old Jalview Archive format
-      try
-      {
-        InputStreamReader in = new InputStreamReader(new FileInputStream(
-                file), "UTF-8");
-  
-        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-  
-        jucs = JalviewUserColours.unmarshal(in);
-  
-        newColours = new Color[jucs.getColourCount()];
-  
-        for (int i = 0; i < 24; i++)
-        {
-          newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
-                  .getRGB(), 16));
-        }
-        ucs = new UserColourScheme(newColours);
-        ucs.setName(jucs.getSchemeName());
-      } catch (Exception ex2)
-      {
-        ex2.printStackTrace();
-      }
-  
-      if (newColours == null)
-      {
-        System.out.println("Error loading User ColourFile\n" + ex);
-      }
-    }
-  
-    return ucs;
-  }
 }
diff --git a/src/jalview/structure/AtomSpec.java b/src/jalview/structure/AtomSpec.java
index a19acef..f20cd31 100644
--- a/src/jalview/structure/AtomSpec.java
+++ b/src/jalview/structure/AtomSpec.java
@@ -29,9 +29,8 @@ package jalview.structure;
  */
 public class AtomSpec
 {
-  // TODO clarify do we want pdbFile here, or pdbId?
-  // compare highlightAtom in 2.8.2 for JalviewJmolBinding and
-  // javascript.MouseOverStructureListener
+  int modelNo;
+
   private String pdbFile;
 
   private String chain;
@@ -41,6 +40,60 @@ public class AtomSpec
   private int atomIndex;
 
   /**
+   * Parses a Chimera atomspec e.g. #1:12.A to construct an AtomSpec model (with
+   * null pdb file name)
+   * 
+   * @param spec
+   * @return
+   * @throw IllegalArgumentException if the spec cannot be parsed, or represents
+   *        more than one residue
+   */
+  public static AtomSpec fromChimeraAtomspec(String spec)
+  {
+    int colonPos = spec.indexOf(":");
+    if (colonPos == -1)
+    {
+      throw new IllegalArgumentException(spec);
+    }
+
+    int hashPos = spec.indexOf("#");
+    if (hashPos == -1 && colonPos != 0)
+    {
+      // # is missing but something precedes : - reject
+      throw new IllegalArgumentException(spec);
+    }
+
+    String modelSubmodel = spec.substring(hashPos + 1, colonPos);
+    int dotPos = modelSubmodel.indexOf(".");
+    int modelId = 0;
+    try
+    {
+      modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
+              : modelSubmodel.substring(0, dotPos));
+    } catch (NumberFormatException e)
+    {
+      // ignore, default to model 0
+    }
+
+    String residueChain = spec.substring(colonPos + 1);
+    dotPos = residueChain.indexOf(".");
+    int resNum = 0;
+    try
+    {
+      resNum = Integer.parseInt(dotPos == -1 ? residueChain
+              : residueChain.substring(0, dotPos));
+    } catch (NumberFormatException e)
+    {
+      // could be a range e.g. #1:4-7.B
+      throw new IllegalArgumentException(spec);
+    }
+
+    String chainId = dotPos == -1 ? "" : residueChain.substring(dotPos + 1);
+
+    return new AtomSpec(modelId, chainId, resNum, 0);
+  }
+
+  /**
    * Constructor
    * 
    * @param pdbFile
@@ -56,6 +109,22 @@ public class AtomSpec
     this.atomIndex = atomNo;
   }
 
+  /**
+   * Constructor
+   * 
+   * @param modelId
+   * @param chainId
+   * @param resNo
+   * @param atomNo
+   */
+  public AtomSpec(int modelId, String chainId, int resNo, int atomNo)
+  {
+    this.modelNo = modelId;
+    this.chain = chainId;
+    this.pdbResNum = resNo;
+    this.atomIndex = atomNo;
+  }
+
   public String getPdbFile()
   {
     return pdbFile;
@@ -76,6 +145,16 @@ public class AtomSpec
     return atomIndex;
   }
 
+  public int getModelNumber()
+  {
+    return modelNo;
+  }
+
+  public void setPdbFile(String file)
+  {
+    pdbFile = file;
+  }
+
   @Override
   public String toString()
   {
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 78634e0..40789ed 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -23,7 +23,9 @@ package jalview.structure;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 
 public class StructureMapping
 {
@@ -47,6 +49,18 @@ public class StructureMapping
   // and atomNo
   HashMap<Integer, int[]> mapping;
 
+  /**
+   * Constructor
+   * 
+   * @param seq
+   * @param pdbfile
+   * @param pdbid
+   * @param chain
+   * @param mapping
+   *          a map from sequence to two values, { resNo, atomNo } in the
+   *          structure
+   * @param mappingDetails
+   */
   public StructureMapping(SequenceI seq, String pdbfile, String pdbid,
           String chain, HashMap<Integer, int[]> mapping,
           String mappingDetails)
@@ -111,6 +125,70 @@ public class StructureMapping
   }
 
   /**
+   * Returns a (possibly empty) list of [start, end] residue positions in the
+   * mapped structure, corresponding to the given range of sequence positions
+   * 
+   * @param fromSeqPos
+   * @param toSeqPos
+   * @return
+   */
+  public List<int[]> getPDBResNumRanges(int fromSeqPos, int toSeqPos)
+  {
+    List<int[]> result = new ArrayList<int[]>();
+    int startRes = -1;
+    int endRes = -1;
+
+    for (int i = fromSeqPos; i <= toSeqPos; i++)
+    {
+      int resNo = getPDBResNum(i);
+      if (resNo == UNASSIGNED_VALUE)
+      {
+        continue; // no mapping from this sequence position
+      }
+      if (startRes == -1)
+      {
+        startRes = resNo;
+        endRes = resNo;
+      }
+      if (resNo >= startRes && resNo <= endRes)
+      {
+        // within the current range - no change
+        continue;
+      }
+      if (resNo == startRes - 1)
+      {
+        // extend beginning of current range
+        startRes--;
+        continue;
+      }
+      if (resNo == endRes + 1)
+      {
+        // extend end of current range
+        endRes++;
+        continue;
+      }
+
+      /*
+       * resNo is not within or contiguous with last range,
+       * so write out the last range
+       */
+      result.add(new int[] { startRes, endRes });
+      startRes = resNo;
+      endRes = resNo;
+    }
+
+    /*
+     * and add the last range
+     */
+    if (startRes != -1)
+    {
+      result.add(new int[] { startRes, endRes });
+    }
+
+    return result;
+  }
+
+  /**
    * 
    * @param pdbResNum
    * @return -1 or the corresponding sequence position for a pdb residue number
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 65fd5e7..3ab642f 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -589,11 +589,9 @@ public class StructureSelectionManager
     return pdb;
   }
 
-  private boolean isCIFFile(String filename)
+  public void addStructureMapping(StructureMapping sm)
   {
-    String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
-            filename.length());
-    return "cif".equalsIgnoreCase(fileExt);
+    mappings.add(sm);
   }
 
   /**
@@ -806,6 +804,27 @@ public class StructureSelectionManager
       return;
     }
 
+    SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+    for (Object li : listeners)
+    {
+      if (li instanceof SequenceListener)
+      {
+        ((SequenceListener) li).highlightSequence(results);
+      }
+    }
+  }
+
+  /**
+   * Constructs a SearchResults object holding regions (if any) in the Jalview
+   * alignment which have a mapping to the structure viewer positions in the
+   * supplied list
+   * 
+   * @param atoms
+   * @return
+   */
+  public SearchResultsI findAlignmentPositionsForStructurePositions(
+          List<AtomSpec> atoms)
+  {
     SearchResultsI results = new SearchResults();
     for (AtomSpec atom : atoms)
     {
@@ -831,13 +850,7 @@ public class StructureSelectionManager
         }
       }
     }
-    for (Object li : listeners)
-    {
-      if (li instanceof SequenceListener)
-      {
-        ((SequenceListener) li).highlightSequence(results);
-      }
-    }
+    return results;
   }
 
   /**
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index fda08fd..84475fe 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -21,7 +21,6 @@
 package jalview.structures.models;
 
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
@@ -42,6 +41,7 @@ import jalview.util.MessageManager;
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
 /**
@@ -521,15 +521,15 @@ public abstract class AAStructureBindingModel extends
    *          the sequence alignment which is the basis of structure
    *          superposition
    * @param matched
-   *          an array of booleans, indexed by alignment column, where true
-   *          indicates that every structure has a mapped residue present in the
-   *          column (so the column can participate in structure alignment)
+   *          a BitSet, where bit j is set to indicate that every structure has
+   *          a mapped residue present in column j (so the column can
+   *          participate in structure alignment)
    * @param structures
    *          an array of data beans corresponding to pdb file index
    * @return
    */
   protected int findSuperposableResidues(AlignmentI alignment,
-          boolean[] matched, SuperposeData[] structures)
+          BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
     String[] files = getPdbFile();
@@ -559,16 +559,16 @@ public abstract class AAStructureBindingModel extends
             {
               refStructure = pdbfnum;
             }
-            for (int r = 0; r < matched.length; r++)
+            for (int r = 0; r < alignment.getWidth(); r++)
             {
-              if (!matched[r])
+              if (!matched.get(r))
               {
                 continue;
               }
               int pos = getMappedPosition(theSequence, r, mapping);
               if (pos < 1 || pos == lastPos)
               {
-                matched[r] = false;
+                matched.clear(r);
                 continue;
               }
               lastPos = pos;
@@ -700,24 +700,29 @@ public abstract class AAStructureBindingModel extends
 
   public abstract void setJalviewColourScheme(ColourSchemeI cs);
 
-  public abstract void superposeStructures(AlignmentI[] als, int[] alm,
-          ColumnSelection[] alc);
-
-  public abstract void setBackgroundColour(Color col);
-
-  protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment);
-
   /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
+   * Constructs and sends a command to align structures against a reference
+   * structure, based on one or more sequence alignments. May optionally return
+   * an error or warning message for the alignment command.
    * 
+   * @param alignments
+   *          an array of alignments to process
+   * @param structureIndices
+   *          an array of corresponding reference structures (index into pdb
+   *          file array); if a negative value is passed, the first PDB file
+   *          mapped to an alignment sequence is used as the reference for
+   *          superposition
+   * @param hiddenCols
+   *          an array of corresponding hidden columns for each alignment
    * @return
    */
-  public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+  public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
+          ColumnSelection[] hiddenCols);
+
+  public abstract void setBackgroundColour(Color col);
+
+  protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
+          String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
 
   /**
    * returns the current sequenceRenderer that should be used to colour the
@@ -743,8 +748,6 @@ public abstract class AAStructureBindingModel extends
    */
   public void colourBySequence(AlignmentViewPanel alignmentv)
   {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
     if (!colourBySequence || !isLoadingFinished())
     {
       return;
@@ -757,15 +760,8 @@ public abstract class AAStructureBindingModel extends
   
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
   
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-  
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, sr, fr, alignment);
+            files, sr, alignmentv);
     colourBySequence(colourBySequenceCommands);
   }
 
@@ -773,4 +769,7 @@ public abstract class AAStructureBindingModel extends
   {
     return fileLoadingError != null && fileLoadingError.length() > 0;
   }
+
+  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment);
 }
diff --git a/src/jalview/util/RangeComparator.java b/src/jalview/util/RangeComparator.java
new file mode 100644
index 0000000..f911a9b
--- /dev/null
+++ b/src/jalview/util/RangeComparator.java
@@ -0,0 +1,25 @@
+package jalview.util;
+
+import java.util.Comparator;
+
+/**
+ * A comparator to order [from, to] ranges into ascending or descending order of
+ * their start position
+ */
+public class RangeComparator implements Comparator<int[]>
+{
+  boolean forwards;
+
+  public RangeComparator(boolean forward)
+  {
+    forwards = forward;
+  }
+
+  @Override
+  public int compare(int[] o1, int[] o2)
+  {
+    int compared = Integer.compare(o1[0], o2[0]);
+    return forwards ? compared : -compared;
+  }
+
+}
\ No newline at end of file
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 6dcf26d..47dceec 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,6 +20,17 @@
  */
 package jalview.viewmodel;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -57,17 +68,6 @@ import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -78,6 +78,8 @@ import java.util.Map;
 public abstract class AlignmentViewport implements AlignViewportI,
         CommandListener, VamsasSource
 {
+  protected ViewportRanges ranges;
+
   protected ViewStyleI viewStyle = new ViewStyle();
 
   /**
@@ -672,6 +674,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   protected AlignmentAnnotation complementConsensus;
 
+  protected AlignmentAnnotation gapcounts;
+
   protected AlignmentAnnotation strucConsensus;
 
   protected AlignmentAnnotation conservation;
@@ -774,6 +778,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
   }
 
   @Override
+  public AlignmentAnnotation getAlignmentGapAnnotation()
+  {
+    return gapcounts;
+  }
+
+  @Override
   public AlignmentAnnotation getComplementConsensusAnnotation()
   {
     return complementConsensus;
@@ -813,7 +823,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
+    if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
     {
       return;
     }
@@ -1285,15 +1295,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean followHighlight = true;
 
-  // TODO private with getters and setters?
-  public int startRes;
-
-  public int endRes;
-
-  public int startSeq;
-
-  public int endSeq;
-
   /**
    * Property change listener for changes in alignment
    * 
@@ -1892,6 +1893,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
       consensus = new AlignmentAnnotation("Consensus", "PID",
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
+      gapcounts = new AlignmentAnnotation("Occupancy",
+              "Number of aligned positions",
+              new Annotation[1], 0f, alignment.getHeight(),
+              AlignmentAnnotation.BAR_GRAPH);
+      initGapCounts(gapcounts);
 
       initComplementConsensus();
     }
@@ -1946,6 +1952,20 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
   }
 
+  // these should be extracted from the view model - style and settings for
+  // derived annotation
+  private void initGapCounts(AlignmentAnnotation counts)
+  {
+    counts.hasText = false;
+    counts.autoCalculated = true;
+    counts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+    if (showConsensus)
+    {
+      alignment.addAnnotation(counts);
+    }
+  }
+
   private void initConservation()
   {
     if (showConservation)
@@ -2647,63 +2667,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
     this.followHighlight = b;
   }
 
-  public int getStartRes()
-  {
-    return startRes;
-  }
-
   @Override
-  public int getEndRes()
-  {
-    return endRes;
-  }
-
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
-
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
-
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
-
-  public void setEndRes(int res)
+  public ViewportRanges getRanges()
   {
-    if (res > alignment.getWidth() - 1)
-    {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " +
-      // (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
-    }
-    if (res < 0)
-    {
-      res = 0;
-    }
-    this.endRes = res;
-  }
-
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
-    {
-      seq = alignment.getHeight();
-    }
-    if (seq < 0)
-    {
-      seq = 0;
-    }
-    this.endSeq = seq;
-  }
-
-  public int getEndSeq()
-  {
-    return endSeq;
+    return ranges;
   }
 
   /**
@@ -2743,7 +2710,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
      * locate 'middle' column (true middle if an odd number visible, left of
      * middle if an even number visible)
      */
-    int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
+    int middleColumn = ranges.getStartRes()
+            + (ranges.getEndRes() - ranges.getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
 
@@ -2753,7 +2721,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
-    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+    for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2821,7 +2789,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   private boolean selectionIsDefinedGroup = false;
 
-
   @Override
   public boolean isSelectionDefinedGroup()
   {
diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
new file mode 100644
index 0000000..43680b5
--- /dev/null
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -0,0 +1,343 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.viewmodel;
+
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenSequences;
+
+import java.awt.Graphics;
+
+public class OverviewDimensions
+{
+  // Default width and height values
+  private static final int DEFAULT_GRAPH_HEIGHT = 20;
+
+  private static final int MAX_WIDTH = 400;
+
+  private static final int MIN_WIDTH = 120;
+
+  private static final int MIN_SEQ_HEIGHT = 40;
+
+  private static final int MAX_SEQ_HEIGHT = 300;
+
+  // width of the overview panel
+  private int width;
+
+  // height of sequences part of the overview panel
+  private int sequencesHeight;
+
+  // height of the graphs part of the overview panel
+  private int graphHeight = DEFAULT_GRAPH_HEIGHT;
+
+  // dimensions of box outlining current extent of view in alignment panel
+  // location of left side of box
+  private int boxX = -1;
+
+  // location of bottom of box
+  private int boxY = -1;
+
+  // width of box
+  private int boxWidth = -1;
+
+  // height of box
+  private int boxHeight = -1;
+
+  // scroll position in viewport corresponding to boxX
+  private int scrollCol = -1;
+
+  // scroll position in viewport corresponding to boxY
+  private int scrollRow = -1;
+
+  /**
+   * Create an OverviewDimensions object
+   * 
+   * @param ranges
+   *          positional properties of the viewport
+   * @param showAnnotationPanel
+   *          true if the annotation panel is to be shown, false otherwise
+   */
+  public OverviewDimensions(ViewportRanges ranges,
+          boolean showAnnotationPanel)
+  {
+    // scale the initial size of overviewpanel to shape of alignment
+    float initialScale = (float) ranges.getAbsoluteAlignmentWidth()
+            / (float) ranges.getAbsoluteAlignmentHeight();
+
+    if (!showAnnotationPanel)
+    {
+      graphHeight = 0;
+    }
+
+    if (ranges.getAbsoluteAlignmentWidth() > ranges
+            .getAbsoluteAlignmentHeight())
+    {
+      // wider
+      width = MAX_WIDTH;
+      sequencesHeight = Math.round(MAX_WIDTH / initialScale);
+      if (sequencesHeight < MIN_SEQ_HEIGHT)
+      {
+        sequencesHeight = MIN_SEQ_HEIGHT;
+      }
+    }
+    else
+    {
+      // taller
+      width = Math.round(MAX_WIDTH * initialScale);
+      sequencesHeight = MAX_SEQ_HEIGHT;
+
+      if (width < MIN_WIDTH)
+      {
+        width = MIN_WIDTH;
+      }
+    }
+  }
+
+  /**
+   * Check box dimensions and scroll positions and correct if necessary
+   * 
+   * @param mousex
+   *          x position in overview panel
+   * @param mousey
+   *          y position in overview panel
+   * @param hiddenSeqs
+   *          hidden sequences
+   * @param hiddenCols
+   *          hidden columns
+   * @param ranges
+   *          viewport position properties
+   */
+  public void updateViewportFromMouse(int mousex, int mousey,
+          HiddenSequences hiddenSeqs, ColumnSelection hiddenCols,
+          ViewportRanges ranges)
+  {
+    int x = mousex;
+    int y = mousey;
+
+    int alwidth = ranges.getAbsoluteAlignmentWidth();
+    int alheight = ranges.getAbsoluteAlignmentHeight();
+
+    if (x < 0)
+    {
+      x = 0;
+    }
+
+    if (y < 0)
+    {
+      y = 0;
+    }
+
+    //
+    // Convert x value to residue position
+    //
+
+    // need to determine where scrollCol should be, given x
+    // to do this also need to know width of viewport, and some hidden column
+    // correction
+
+    // convert x to residues - this is an absolute position
+    int xAsRes = Math.round((float) x * alwidth / width);
+
+    // get viewport width in residues
+    int vpwidth = ranges.getEndRes() - ranges.getStartRes() + 1;
+
+    // get where x should be when accounting for hidden cols
+    // if x is in a hidden col region, shift to left - but we still need
+    // absolute position
+    // so convert back after getting visible region position
+    int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+
+    // check in case we went off the edge of the alignment
+    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    if (visXAsRes + vpwidth - 1 > visAlignWidth)
+    {
+      // went past the end of the alignment, adjust backwards
+
+      // if last position was before the end of the alignment, need to update
+      if ((scrollCol + vpwidth - 1) < visAlignWidth)
+      {
+        visXAsRes = hiddenCols.findColumnPosition(hiddenCols
+                .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
+      }
+      else
+      {
+        visXAsRes = scrollCol;
+      }
+    }
+
+    //
+    // Convert y value to sequence position
+    //
+
+    // convert y to residues
+    int yAsSeq = Math.round((float) y * alheight / sequencesHeight);
+
+    // get viewport height in sequences
+    // add 1 because height includes both endSeq and startSeq
+    int vpheight = ranges.getEndSeq() - ranges.getStartSeq() + 1;
+
+    // get where y should be when accounting for hidden rows
+    // if y is in a hidden row region, shift up - but we still need absolute
+    // position,
+    // so convert back after getting visible region position
+    yAsSeq = hiddenSeqs.adjustForHiddenSeqs(hiddenSeqs
+            .findIndexWithoutHiddenSeqs(yAsSeq));
+
+    // check in case we went off the edge of the alignment
+    int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
+    int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
+    if (visYAsRes + vpheight - 1 > visAlignHeight)
+    {
+      // went past the end of the alignment, adjust backwards
+      if ((scrollRow + vpheight - 1) < visAlignHeight)
+      {
+        visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(hiddenSeqs
+                .subtractVisibleRows(vpheight - 1, alheight - 1));
+      }
+      else
+      {
+        visYAsRes = scrollRow;
+      }
+    }
+
+    // update scroll values
+    scrollCol = visXAsRes;
+    scrollRow = visYAsRes;
+
+  }
+
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   * @param hiddenSeqs
+   *          hidden sequences
+   * @param hiddenCols
+   *          hidden columns
+   * @param ranges
+   *          viewport position properties
+   */
+  public void setBoxPosition(HiddenSequences hiddenSeqs,
+          ColumnSelection hiddenCols, ViewportRanges ranges)
+  {
+    int alwidth = ranges.getAbsoluteAlignmentWidth();
+    int alheight = ranges.getAbsoluteAlignmentHeight();
+
+    // work with absolute values of startRes and endRes
+    int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
+    int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
+
+    // work with absolute values of startSeq and endSeq
+    int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
+    int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
+
+    // boxX, boxY is the x,y location equivalent to startRes, startSeq
+    boxX = Math.round((float) startRes * width / alwidth);
+    boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+
+    // boxWidth is the width in residues translated to pixels
+    // since the box includes both the start and end residues, add 1 to the
+    // difference
+    boxWidth = Math
+            .round((float) (endRes - startRes + 1) * width / alwidth);
+    // boxHeight is the height in sequences translated to pixels
+    boxHeight = Math.round((float) (endSeq - startSeq + 1)
+            * sequencesHeight
+            / alheight);
+  }
+
+  /**
+   * Draw the overview panel's viewport box on a graphics object
+   * 
+   * @param g
+   *          the graphics object to draw on
+   */
+  public void drawBox(Graphics g)
+  {
+    g.drawRect(boxX, boxY, boxWidth, boxHeight);
+    g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+  }
+
+  public int getScrollCol()
+  {
+    return scrollCol;
+  }
+
+  public int getScrollRow()
+  {
+    return scrollRow;
+  }
+
+  // TODO should be removed, when unit test has mock Graphics object available
+  // to check boxX/boxY
+  public int getBoxX()
+  {
+    return boxX;
+  }
+
+  // TODO should be removed, when unit test has mock Graphics object available
+  // to check boxX/boxY
+  public int getBoxY()
+  {
+    return boxY;
+  }
+
+  // TODO should be removed, when unit test has mock Graphics object available
+  public int getBoxWidth()
+  {
+    return boxWidth;
+  }
+
+  // TODO should be removed, when unit test has mock Graphics object available
+  public int getBoxHeight()
+  {
+    return boxHeight;
+  }
+
+  public void setWidth(int w)
+  {
+    width = w;
+  }
+
+  public void setHeight(int h)
+  {
+    sequencesHeight = h - graphHeight;
+  }
+
+  public int getWidth()
+  {
+    return width;
+  }
+
+  public int getHeight()
+  {
+    return sequencesHeight + graphHeight;
+  }
+
+  public int getSequencesHeight()
+  {
+    return sequencesHeight;
+  }
+
+  public int getGraphHeight()
+  {
+    return graphHeight;
+  }
+}
diff --git a/src/jalview/viewmodel/ViewportProperties.java b/src/jalview/viewmodel/ViewportProperties.java
new file mode 100644
index 0000000..246806e
--- /dev/null
+++ b/src/jalview/viewmodel/ViewportProperties.java
@@ -0,0 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.viewmodel;
+
+public abstract class ViewportProperties
+{
+
+}
diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
new file mode 100644
index 0000000..c91d2d9
--- /dev/null
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -0,0 +1,188 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.viewmodel;
+
+import jalview.datamodel.AlignmentI;
+
+/**
+ * Embryonic class which: Supplies and updates viewport properties relating to
+ * position such as: start and end residues and sequences; ideally will serve
+ * hidden columns/rows too. Intention also to support calculations for
+ * positioning, scrolling etc. such as finding the middle of the viewport,
+ * checking for scrolls off screen
+ */
+public class ViewportRanges extends ViewportProperties
+{
+  // start residue of viewport
+  private int startRes;
+
+  // end residue of viewport
+  private int endRes;
+
+  // start sequence of viewport
+  private int startSeq;
+
+  // end sequence of viewport
+  private int endSeq;
+
+  // alignment
+  private AlignmentI al;
+
+  /**
+   * Constructor
+   * 
+   * @param alignment
+   *          the viewport's alignment
+   */
+  public ViewportRanges(AlignmentI alignment)
+  {
+    // initial values of viewport settings
+    this.startRes = 0;
+    this.endRes = alignment.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = alignment.getHeight() - 1;
+    this.al = alignment;
+  }
+
+  /**
+   * Get alignment width in cols, including hidden cols
+   */
+  public int getAbsoluteAlignmentWidth()
+  {
+    return al.getWidth();
+  }
+
+  /**
+   * Get alignment height in rows, including hidden rows
+   */
+  public int getAbsoluteAlignmentHeight()
+  {
+    return al.getHeight() + al.getHiddenSequences().getSize();
+  }
+
+  /**
+   * Set first residue visible in the viewport
+   * 
+   * @param res
+   *          residue position
+   */
+  public void setStartRes(int res)
+  {
+    if (res > al.getWidth() - 1)
+    {
+      res = al.getWidth() - 1;
+    }
+    else if (res < 0)
+    {
+      res = 0;
+    }
+    this.startRes = res;
+  }
+
+  /**
+   * Set last residue visible in the viewport
+   * 
+   * @param res
+   *          residue position
+   */
+  public void setEndRes(int res)
+  {
+    if (res >= al.getWidth())
+    {
+      res = al.getWidth() - 1;
+    }
+    else if (res < 0)
+    {
+      res = 0;
+    }
+    this.endRes = res;
+  }
+
+  /**
+   * Set the first sequence visible in the viewport
+   * 
+   * @param seq
+   *          sequence position
+   */
+  public void setStartSeq(int seq)
+  {
+    if (seq > al.getHeight() - 1)
+    {
+      seq = al.getHeight() - 1;
+    }
+    else if (seq < 0)
+    {
+      seq = 0;
+    }
+    this.startSeq = seq;
+  }
+
+  /**
+   * Set the last sequence visible in the viewport
+   * 
+   * @param seq
+   *          sequence position
+   */
+  public void setEndSeq(int seq)
+  {
+    if (seq >= al.getHeight())
+    {
+      seq = al.getHeight() - 1;
+    }
+    else if (seq < 0)
+    {
+      seq = 0;
+    }
+    this.endSeq = seq;
+  }
+
+  /**
+   * Get start residue of viewport
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  /**
+   * Get end residue of viewport
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  /**
+   * Get start sequence of viewport
+   */
+  public int getStartSeq()
+  {
+    return startSeq;
+  }
+
+  /**
+   * Get end sequence of viewport
+   */
+  public int getEndSeq()
+  {
+    return endSeq;
+  }
+}
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 8468329..84c9477 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -550,11 +550,13 @@ public abstract class FeatureRendererModel implements
   }
 
   /**
-   * calculate the render colour for a specific feature using current feature
-   * settings.
+   * Returns the configured colour for a particular feature instance. This
+   * includes calculation of 'colour by label', or of a graduated score colour,
+   * if applicable. It does not take into account feature visibility or colour
+   * transparency.
    * 
    * @param feature
-   * @return render colour for the given feature
+   * @return
    */
   public Color getColour(SequenceFeature feature)
   {
@@ -586,11 +588,13 @@ public abstract class FeatureRendererModel implements
     featureColours.put(featureType, col);
   }
 
+  @Override
   public void setTransparency(float value)
   {
     transparency = value;
   }
 
+  @Override
   public float getTransparency()
   {
     return transparency;
@@ -822,7 +826,7 @@ public abstract class FeatureRendererModel implements
    * @return list of groups
    */
   @Override
-  public List getGroups(boolean visible)
+  public List<String> getGroups(boolean visible)
   {
     if (featureGroups != null)
     {
diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 0c7e69a..284f1a1 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -50,7 +50,8 @@ public class ConsensusThread extends AlignCalcWorker
     try
     {
       AlignmentAnnotation consensus = getConsensusAnnotation();
-      if (consensus == null || calcMan.isPending(this))
+      AlignmentAnnotation gap = getGapAnnotation();
+      if ((consensus == null && gap == null) || calcMan.isPending(this))
       {
         calcMan.workerComplete(this);
         return;
@@ -117,6 +118,11 @@ public class ConsensusThread extends AlignCalcWorker
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
     consensus.annotations = new Annotation[aWidth];
+    AlignmentAnnotation gap = getGapAnnotation();
+    if (gap != null)
+    {
+      gap.annotations = new Annotation[aWidth];
+    }
   }
 
   /**
@@ -127,8 +133,8 @@ public class ConsensusThread extends AlignCalcWorker
 
     SequenceI[] aseqs = getSequences();
     int width = alignment.getWidth();
-    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0,
-            width, true);
+    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+            true);
 
     alignViewport.setSequenceConsensusHash(hconsensus);
     setColourSchemeConsensus(hconsensus);
@@ -165,6 +171,16 @@ public class ConsensusThread extends AlignCalcWorker
   }
 
   /**
+   * Get the Gap annotation for the alignment
+   * 
+   * @return
+   */
+  protected AlignmentAnnotation getGapAnnotation()
+  {
+    return alignViewport.getAlignmentGapAnnotation();
+  }
+
+  /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
@@ -182,6 +198,11 @@ public class ConsensusThread extends AlignCalcWorker
             && hconsensus != null)
     {
       deriveConsensus(consensus, hconsensus);
+      AlignmentAnnotation gap = getGapAnnotation();
+      if (gap != null)
+      {
+        deriveGap(gap, hconsensus);
+      }
     }
   }
 
@@ -200,13 +221,29 @@ public class ConsensusThread extends AlignCalcWorker
 
     long nseq = getSequences().length;
     AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
-            hconsensus.getStartColumn(),
-            hconsensus.getEndColumn() + 1,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
             alignViewport.isIgnoreGapsConsensus(),
             alignViewport.isShowSequenceLogo(), nseq);
   }
 
   /**
+   * Convert the computed consensus data into a gap annotation row for display.
+   * 
+   * @param gapAnnotation
+   *          the annotation to be populated
+   * @param hconsensus
+   *          the computed consensus data
+   */
+  protected void deriveGap(AlignmentAnnotation gapAnnotation,
+          ProfilesI hconsensus)
+  {
+    long nseq = getSequences().length;
+    AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+            nseq);
+  }
+
+  /**
    * Get the consensus data stored on the viewport.
    * 
    * @return
diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 676a4b6..4d3dd2f 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -617,8 +617,8 @@ public class DasSequenceFeatureFetcher
     }
     af.getFeatureRenderer().featuresAdded();
 
-    int start = af.getViewport().getStartSeq();
-    int end = af.getViewport().getEndSeq();
+    int start = af.getViewport().getRanges().getStartSeq();
+    int end = af.getViewport().getRanges().getEndSeq();
     int index;
     for (index = start; index < end; index++)
     {
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 8bae5ba..ea65125 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -74,6 +74,12 @@ import MCview.PDBChain;
 
 public class SiftsClient implements SiftsClientI
 {
+  /*
+   * for use in mocking out file fetch for tests only
+   * - reset to null after testing!
+   */
+  private static File mockSiftsFile;
+
   private Entry siftsEntry;
 
   private StructureFile pdb;
@@ -187,6 +193,14 @@ public class SiftsClient implements SiftsClientI
    */
   public static File getSiftsFile(String pdbId) throws SiftsException
   {
+    /*
+     * return mocked file if it has been set
+     */
+    if (mockSiftsFile != null)
+    {
+      return mockSiftsFile;
+    }
+
     String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
             + pdbId.toLowerCase() + ".xml.gz";
     File siftsFile = new File(siftsFileName);
@@ -1097,4 +1111,9 @@ public class SiftsClient implements SiftsClientI
     return siftsEntry.getDbVersion();
   }
 
+  public static void setMockSiftsFile(File file)
+  {
+    mockSiftsFile = file;
+  }
+
 }
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 7af77f5..68933bd 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentGenerator;
 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
@@ -1196,4 +1197,67 @@ public class AlignmentTest
     assertNull(a.findGroup(seq2, 8));
   }
 
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceByIndex()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete -ve index, nothing happens
+    a.deleteSequence(-1);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete beyond end of alignment, nothing happens
+    a.deleteSequence(14);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteSequenceBySeq()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete sequence 10, alignment reduced by 1
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(10);
+    a.deleteSequence(seq);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+
+    // try to delete non-existent sequence, nothing happens
+    seq = new Sequence("cds", "GCCTCGGAT");
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteHiddenSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI a = gen.generate(20, 15, 123, 5, 5);
+
+    // delete a sequence which is hidden, check it is NOT removed from hidden
+    // sequences
+    int height = a.getAbsoluteHeight();
+    SequenceI seq = a.getSequenceAt(2);
+    a.getHiddenSequences().hideSequence(seq);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+    a.deleteSequence(2);
+    assertEquals(a.getAbsoluteHeight(), height - 1);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+
+    // delete a sequence which is not hidden, check hiddenSequences are not
+    // affected
+    a.deleteSequence(10);
+    assertEquals(a.getAbsoluteHeight(), height - 2);
+    assertEquals(a.getHiddenSequences().getSize(), 1);
+  }
+
 }
diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 1d819c9..4d3f611 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -105,9 +105,97 @@ public class ColumnSelectionTest
     cs.hideColumns(4, 4);
     assertEquals(4, cs.findColumnPosition(5));
 
+    // hiding column 4 moves column 4 to position 3
+    assertEquals(3, cs.findColumnPosition(4));
+
     // hiding columns 1 and 2 moves column 5 to column 2
     cs.hideColumns(1, 2);
     assertEquals(2, cs.findColumnPosition(5));
+
+    // check with > 1 hidden column regions
+    // where some columns are in the hidden regions
+    ColumnSelection cs2 = new ColumnSelection();
+    cs2.hideColumns(5, 10);
+    cs2.hideColumns(20, 27);
+    cs2.hideColumns(40, 44);
+
+    // hiding columns 5-10 and 20-27 moves column 8 to column 4
+    assertEquals(4, cs2.findColumnPosition(8));
+
+    // and moves column 24 to 13
+    assertEquals(13, cs2.findColumnPosition(24));
+
+    // and moves column 28 to 14
+    assertEquals(14, cs2.findColumnPosition(28));
+
+    // and moves column 40 to 25
+    assertEquals(25, cs2.findColumnPosition(40));
+
+    // check when hidden columns start at 0 that the visible column
+    // is returned as 0
+    ColumnSelection cs3 = new ColumnSelection();
+    cs3.hideColumns(0, 4);
+    assertEquals(0, cs3.findColumnPosition(2));
+
+  }
+
+  /**
+   * Test the method that finds the visible column position a given distance
+   * before another column
+   */
+  @Test(groups = { "Functional" })
+  public void testFindColumnNToLeft()
+  {
+    ColumnSelection cs = new ColumnSelection();
+
+    // test that without hidden columns, findColumnNToLeft returns
+    // position n to left of provided position
+    int pos = cs.subtractVisibleColumns(3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = cs.subtractVisibleColumns(0, 10);
+    assertEquals(10, pos);
+
+    // overflow to left returns negative number
+    pos = cs.subtractVisibleColumns(3, 0);
+    assertEquals(-3, pos);
+
+    // test that with hidden columns to left of result column
+    // behaviour is the same as above
+    cs.hideColumns(1, 3);
+
+    // position n to left of provided position
+    pos = cs.subtractVisibleColumns(3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = cs.subtractVisibleColumns(0, 10);
+    assertEquals(10, pos);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.subtractVisibleColumns(8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.subtractVisibleColumns(8, 23);
+    assertEquals(9, pos);
+
+    // repeat last 2 tests with no hidden columns to left of required position
+    cs.revealAllHiddenColumns();
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.subtractVisibleColumns(8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.subtractVisibleColumns(8, 23);
+    assertEquals(9, pos);
+
   }
 
   /**
diff --git a/test/jalview/datamodel/HiddenSequencesTest.java b/test/jalview/datamodel/HiddenSequencesTest.java
index cae3536..7795988 100644
--- a/test/jalview/datamodel/HiddenSequencesTest.java
+++ b/test/jalview/datamodel/HiddenSequencesTest.java
@@ -49,7 +49,7 @@ public class HiddenSequencesTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  static int SEQ_COUNT = 10;
+  static int SEQ_COUNT = 25;
 
   SequenceI[] seqs;
 
@@ -62,8 +62,9 @@ public class HiddenSequencesTest
     seqs = new SequenceI[SEQ_COUNT];
     for (int i = 0; i < SEQ_COUNT; i++)
     {
-      // sequence lengths are 1, 2, ... 10
-      seqs[i] = new Sequence("Seq" + i, "abcdefghijk".substring(0, i + 1));
+      // sequence lengths are 1, 2, ... 25
+      seqs[i] = new Sequence("Seq" + i,
+              "abcdefghijklmnopqrstuvwxy".substring(0, i + 1));
     }
   }
 
@@ -89,7 +90,7 @@ public class HiddenSequencesTest
     /*
      * alignment is now seq0/2/3/4/7/8/9
      */
-    assertEquals(7, al.getHeight());
+    assertEquals(SEQ_COUNT - 3, al.getHeight());
     assertEquals(0, hs.adjustForHiddenSeqs(0));
     assertEquals(2, hs.adjustForHiddenSeqs(1));
     assertEquals(3, hs.adjustForHiddenSeqs(2));
@@ -193,7 +194,7 @@ public class HiddenSequencesTest
     /*
      * alignment is now seq0/2/3/4/7/8/9
      */
-    assertEquals(7, al.getHeight());
+    assertEquals(SEQ_COUNT - 3, al.getHeight());
     assertEquals(0, hs.findIndexWithoutHiddenSeqs(0));
     assertEquals(0, hs.findIndexWithoutHiddenSeqs(1));
     assertEquals(1, hs.findIndexWithoutHiddenSeqs(2));
@@ -207,6 +208,76 @@ public class HiddenSequencesTest
   }
 
   /**
+   * Test the method that finds the visible row position a given distance before
+   * another row
+   */
+  @Test(groups = { "Functional" })
+  public void testFindIndexNFromRow()
+  {
+    AlignmentI al = new Alignment(seqs);
+    HiddenSequences hs = new HiddenSequences(al);
+
+    // test that without hidden rows, findIndexNFromRow returns
+    // position n above provided position
+    int pos = hs.subtractVisibleRows(3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = hs.subtractVisibleRows(0, 10);
+    assertEquals(10, pos);
+
+    // overflow to top returns negative number
+    pos = hs.subtractVisibleRows(3, 0);
+    assertEquals(-3, pos);
+
+    // test that with hidden rows above result row
+    // behaviour is the same as above
+    hs.hideSequence(seqs[1]);
+    hs.hideSequence(seqs[2]);
+    hs.hideSequence(seqs[3]);
+
+    // position n above provided position
+    pos = hs.subtractVisibleRows(3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = hs.subtractVisibleRows(0, 10);
+    assertEquals(10, pos);
+
+    // test with one set of hidden rows between start and required position
+    hs.hideSequence(seqs[12]);
+    hs.hideSequence(seqs[13]);
+    hs.hideSequence(seqs[14]);
+    hs.hideSequence(seqs[15]);
+    pos = hs.subtractVisibleRows(8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden rows between start and required position
+    hs.hideSequence(seqs[20]);
+    hs.hideSequence(seqs[21]);
+    pos = hs.subtractVisibleRows(8, 23);
+    assertEquals(9, pos);
+
+    // repeat last 2 tests with no hidden columns to left of required position
+    hs.showAll(null);
+
+    // test with one set of hidden rows between start and required position
+    hs.hideSequence(seqs[12]);
+    hs.hideSequence(seqs[13]);
+    hs.hideSequence(seqs[14]);
+    hs.hideSequence(seqs[15]);
+    pos = hs.subtractVisibleRows(8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden rows between start and required position
+    hs.hideSequence(seqs[20]);
+    hs.hideSequence(seqs[21]);
+    pos = hs.subtractVisibleRows(8, 23);
+    assertEquals(9, pos);
+
+  }
+
+  /**
    * Test the method that reconstructs (sort of) the full alignment including
    * hidden sequences
    */
@@ -289,7 +360,7 @@ public class HiddenSequencesTest
     assertTrue(al.getSequences().contains(seqs[1]));
     HiddenSequences hs = al.getHiddenSequences();
     assertEquals(0, hs.getSize());
-    assertEquals(10, al.getHeight());
+    assertEquals(SEQ_COUNT, al.getHeight());
 
     /*
      * hide the second sequence in the alignment
@@ -299,7 +370,7 @@ public class HiddenSequencesTest
     assertTrue(hs.isHidden(seqs[1]));
     assertFalse(al.getSequences().contains(seqs[1]));
     assertEquals(1, hs.getSize());
-    assertEquals(9, al.getHeight());
+    assertEquals(SEQ_COUNT - 1, al.getHeight());
     assertSame(seqs[2], al.getSequenceAt(1));
 
     /*
@@ -312,7 +383,7 @@ public class HiddenSequencesTest
     assertFalse(al.getSequences().contains(seqs[1]));
     assertFalse(al.getSequences().contains(seqs[2]));
     assertEquals(2, hs.getSize());
-    assertEquals(8, al.getHeight());
+    assertEquals(SEQ_COUNT - 2, al.getHeight());
 
     /*
      * perform 'reveal' on what is now the second sequence in the alignment
@@ -323,7 +394,54 @@ public class HiddenSequencesTest
     assertTrue(revealed.contains(seqs[1]));
     assertTrue(revealed.contains(seqs[2]));
     assertEquals(0, hs.getSize());
-    assertEquals(10, al.getHeight());
+    assertEquals(SEQ_COUNT, al.getHeight());
+  }
+
+  /**
+   * Test the method that adds a sequence to the hidden sequences and deletes it
+   * from the alignment, and its converse, where the first hidden sequences are
+   * at the bottom of the alignment (JAL-2437)
+   */
+  @Test(groups = "Functional")
+  public void testHideShowLastSequences()
+  {
+    AlignmentI al = new Alignment(seqs);
+    assertTrue(al.getSequences().contains(seqs[1]));
+    HiddenSequences hs = al.getHiddenSequences();
+    assertEquals(0, hs.getSize());
+    assertEquals(SEQ_COUNT, al.getHeight());
+
+    /*
+     * hide the last sequence in the alignment
+     */
+    hs.hideSequence(seqs[SEQ_COUNT - 1]);
+    assertFalse(hs.isHidden(seqs[SEQ_COUNT - 2]));
+    assertTrue(hs.isHidden(seqs[SEQ_COUNT - 1]));
+    assertFalse(al.getSequences().contains(seqs[SEQ_COUNT - 1]));
+    assertEquals(1, hs.getSize());
+    assertEquals(SEQ_COUNT - 1, al.getHeight());
+
+    /*
+     * hide the third last sequence in the alignment
+     */
+    hs.hideSequence(seqs[SEQ_COUNT - 3]);
+    assertFalse(hs.isHidden(seqs[SEQ_COUNT - 2]));
+    assertTrue(hs.isHidden(seqs[SEQ_COUNT - 3]));
+    assertFalse(al.getSequences().contains(seqs[SEQ_COUNT - 3]));
+    assertEquals(2, hs.getSize());
+    assertEquals(SEQ_COUNT - 2, al.getHeight());
+
+    /*
+     * reveal all the sequences, which should be reinstated in the same order as they started in
+     */
+    hs.showAll(null);
+    assertFalse(hs.isHidden(seqs[SEQ_COUNT - 3]));
+    assertFalse(hs.isHidden(seqs[SEQ_COUNT - 1]));
+    assertEquals(seqs[SEQ_COUNT - 3], al.getSequences().get(SEQ_COUNT - 3));
+    assertEquals(seqs[SEQ_COUNT - 2], al.getSequences().get(SEQ_COUNT - 2));
+    assertEquals(seqs[SEQ_COUNT - 1], al.getSequences().get(SEQ_COUNT - 1));
+    assertEquals(0, hs.getSize());
+    assertEquals(SEQ_COUNT, al.getHeight());
   }
 
   @Test(groups = "Functional")
diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 439e188..3309adf 100644
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -20,16 +20,24 @@
  */
 package jalview.ext.jmol;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
 import jalview.gui.SequenceRenderer;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
+import java.util.HashMap;
+
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -58,6 +66,77 @@ public class JmolCommandsTest
     // need some mappings!
 
     StructureMappingcommandSet[] commands = JmolCommands
-            .getColourBySequenceCommand(ssm, files, seqs, sr, null, al);
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetColourBySequenceCommands_hiddenColumns()
+  {
+    /*
+     * load these sequences, coloured by Strand propensity,
+     * with columns 2-4 hidden
+     */
+    SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
+    SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame af = new AlignFrame(al, 800, 500);
+    af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(2);
+    cs.addElement(3);
+    cs.addElement(4);
+    af.getViewport().setColumnSelection(cs);
+    af.hideSelColumns_actionPerformed(null);
+    SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+    SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
+    String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
+    StructureSelectionManager ssm = new StructureSelectionManager();
+  
+    /*
+     * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
+     */
+    HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+    for (int pos = 1; pos <= seq1.getLength(); pos++)
+    {
+      map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
+    }
+    StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
+            "A", map, null);
+    ssm.addStructureMapping(sm1);
+    StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
+            "B", map, null);
+    ssm.addStructureMapping(sm2);
+  
+    StructureMappingcommandSet[] commands = JmolCommands
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+    assertEquals(commands.length, 2);
+    assertEquals(commands[0].commands.length, 1);
+
+    String chainACommand = commands[0].commands[0];
+    // M colour is #82827d == (130, 130, 125) (see strand.html help page)
+    assertTrue(chainACommand
+            .contains(";select 21:A/1.1;color[130,130,125]"));
+    // H colour is #60609f == (96, 96, 159)
+    assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
+    // hidden columns are Gray (128, 128, 128)
+    assertTrue(chainACommand
+            .contains(";select 23-25:A/1.1;color[128,128,128]"));
+    // S and G are both coloured #4949b6 == (73, 73, 182)
+    assertTrue(chainACommand
+            .contains(";select 26-30:A/1.1;color[73,73,182]"));
+
+    String chainBCommand = commands[1].commands[0];
+    // M colour is #82827d == (130, 130, 125)
+    assertTrue(chainBCommand
+            .contains(";select 21:B/2.1;color[130,130,125]"));
+    // V colour is #ffff00 == (255, 255, 0)
+    assertTrue(chainBCommand
+.contains(";select 22:B/2.1;color[255,255,0]"));
+    // hidden columns are Gray (128, 128, 128)
+    assertTrue(chainBCommand
+            .contains(";select 23-25:B/2.1;color[128,128,128]"));
+    // S and G are both coloured #4949b6 == (73, 73, 182)
+    assertTrue(chainBCommand
+            .contains(";select 26-30:B/2.1;color[73,73,182]"));
   }
 }
diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index 959ecab..995b099 100644
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
@@ -53,8 +54,7 @@ public class JmolViewerTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] {
-        "-noquestionnaire -nonews -props",
+    Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
         "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
   }
 
diff --git a/test/jalview/ext/rbvi/chimera/4zho.pdb b/test/jalview/ext/rbvi/chimera/4zho.pdb
new file mode 100644
index 0000000..e4ee6df
--- /dev/null
+++ b/test/jalview/ext/rbvi/chimera/4zho.pdb
@@ -0,0 +1,3526 @@
+HEADER    ELECTRON TRANSPORT                      26-APR-15   4ZHO              
+TITLE     THE CRYSTAL STRUCTURE OF ARABIDOPSIS FERREDOXIN 2 WITH 2FE-2S CLUSTER 
+COMPND    MOL_ID: 1;                                                            
+COMPND   2 MOLECULE: FERREDOXIN-2, CHLOROPLASTIC;                               
+COMPND   3 CHAIN: A, B;                                                         
+COMPND   4 SYNONYM: ATFD2;                                                      
+COMPND   5 ENGINEERED: YES                                                      
+SOURCE    MOL_ID: 1;                                                            
+SOURCE   2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA;                           
+SOURCE   3 ORGANISM_COMMON: MOUSE-EAR CRESS;                                    
+SOURCE   4 ORGANISM_TAXID: 3702;                                                
+SOURCE   5 GENE: FD2, PETF, PETF1, AT1G60950, T7P1.9;                           
+SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
+SOURCE   7 EXPRESSION_SYSTEM_TAXID: 469008                                      
+KEYWDS    FERREDOXIN 2FE-2S CLUSTER ELECTRON TRANSFER CHLOROPLAST, ELECTRON     
+KEYWDS   2 TRANSPORT                                                            
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    R.GRINTER,I.JOSTS,A.W.ROSZAK,R.J.COGDELL,D.WALKER                     
+REVDAT   2   09-NOV-16 4ZHO    1       JRNL                                     
+REVDAT   1   31-AUG-16 4ZHO    0                                                
+JRNL        AUTH   R.GRINTER,I.JOSTS,K.MOSBAHI,A.W.ROSZAK,R.J.COGDELL,          
+JRNL        AUTH 2 A.M.BONVIN,J.J.MILNER,S.M.KELLY,O.BYRON,B.O.SMITH,D.WALKER   
+JRNL        TITL   STRUCTURE OF THE BACTERIAL PLANT-FERREDOXIN RECEPTOR FUSA.   
+JRNL        REF    NAT COMMUN                    V.   7 13308 2016              
+JRNL        REFN                   ESSN 2041-1723                               
+JRNL        PMID   27796364                                                     
+JRNL        DOI    10.1038/NCOMMS13308                                          
+REMARK   2                                                                      
+REMARK   2 RESOLUTION.    2.34 ANGSTROMS.                                       
+REMARK   3                                                                      
+REMARK   3 REFINEMENT.                                                          
+REMARK   3   PROGRAM     : REFMAC 5.8.0049                                      
+REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON                               
+REMARK   3                                                                      
+REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
+REMARK   3                                                                      
+REMARK   3  DATA USED IN REFINEMENT.                                            
+REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34                           
+REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 60.73                          
+REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
+REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.5                           
+REMARK   3   NUMBER OF REFLECTIONS             : 12221                          
+REMARK   3                                                                      
+REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
+REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
+REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
+REMARK   3   R VALUE     (WORKING + TEST SET) : 0.198                           
+REMARK   3   R VALUE            (WORKING SET) : 0.197                           
+REMARK   3   FREE R VALUE                     : 0.216                           
+REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.900                           
+REMARK   3   FREE R VALUE TEST SET COUNT      : 627                             
+REMARK   3                                                                      
+REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
+REMARK   3   TOTAL NUMBER OF BINS USED           : 20                           
+REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.34                         
+REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.40                         
+REMARK   3   REFLECTION IN BIN     (WORKING SET) : 864                          
+REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 98.58                        
+REMARK   3   BIN R VALUE           (WORKING SET) : 0.2390                       
+REMARK   3   BIN FREE R VALUE SET COUNT          : 39                           
+REMARK   3   BIN FREE R VALUE                    : 0.3090                       
+REMARK   3                                                                      
+REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
+REMARK   3   PROTEIN ATOMS            : 1440                                    
+REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
+REMARK   3   HETEROGEN ATOMS          : 10                                      
+REMARK   3   SOLVENT ATOMS            : 38                                      
+REMARK   3                                                                      
+REMARK   3  B VALUES.                                                           
+REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
+REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 59.55                          
+REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
+REMARK   3    B11 (A**2) : 2.75000                                              
+REMARK   3    B22 (A**2) : 2.75000                                              
+REMARK   3    B33 (A**2) : -5.50000                                             
+REMARK   3    B12 (A**2) : 0.00000                                              
+REMARK   3    B13 (A**2) : 0.00000                                              
+REMARK   3    B23 (A**2) : 0.00000                                              
+REMARK   3                                                                      
+REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
+REMARK   3   ESU BASED ON R VALUE                            (A): 0.229         
+REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.180         
+REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.136         
+REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.808        
+REMARK   3                                                                      
+REMARK   3 CORRELATION COEFFICIENTS.                                            
+REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.949                         
+REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.952                         
+REMARK   3                                                                      
+REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
+REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  1468 ; 0.017 ; 0.019       
+REMARK   3   BOND LENGTHS OTHERS               (A):  1296 ; 0.001 ; 0.020       
+REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  1990 ; 1.933 ; 1.975       
+REMARK   3   BOND ANGLES OTHERS          (DEGREES):  3026 ; 0.912 ; 3.000       
+REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   192 ; 7.288 ; 5.000       
+REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):    66 ;34.298 ;26.970       
+REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   234 ;14.918 ;15.000       
+REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):     2 ; 5.922 ;15.000       
+REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   230 ; 0.115 ; 0.200       
+REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  1682 ; 0.007 ; 0.020       
+REMARK   3   GENERAL PLANES OTHERS             (A):   276 ; 0.001 ; 0.020       
+REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
+REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
+REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
+REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
+REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL       
+REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
+REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
+REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
+REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL       
+REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
+REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL       
+REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL       
+REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
+REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL       
+REMARK   3                                                                      
+REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT      
+REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):   774 ; 3.602 ; 4.642       
+REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):   773 ; 3.584 ; 4.636       
+REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):   964 ; 4.741 ; 6.949       
+REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):   965 ; 4.738 ; 6.957       
+REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):   694 ; 5.685 ; 5.263       
+REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):   691 ; 5.624 ; 5.277       
+REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  NULL ;  NULL ;  NULL       
+REMARK   3   SIDE-CHAIN ANGLE OTHER ATOMS   (A**2):  1021 ; 8.298 ; 7.648       
+REMARK   3   LONG RANGE B REFINED ATOMS     (A**2):  1582 ; 9.824 ;37.488       
+REMARK   3   LONG RANGE B OTHER ATOMS       (A**2):  1580 ; 9.825 ;37.492       
+REMARK   3                                                                      
+REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
+REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL       
+REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL       
+REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL       
+REMARK   3                                                                      
+REMARK   3  NCS RESTRAINTS STATISTICS                                           
+REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL                              
+REMARK   3                                                                      
+REMARK   3  TLS DETAILS                                                         
+REMARK   3   NUMBER OF TLS GROUPS  : 2                                          
+REMARK   3                                                                      
+REMARK   3   TLS GROUP : 1                                                      
+REMARK   3    NUMBER OF COMPONENTS GROUP : 1                                    
+REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI                         
+REMARK   3    RESIDUE RANGE :   A     2        A   118                          
+REMARK   3    ORIGIN FOR THE GROUP (A): -11.9068  -7.9134 -35.1151              
+REMARK   3    T TENSOR                                                          
+REMARK   3      T11:   0.0724 T22:   0.0486                                     
+REMARK   3      T33:   0.0466 T12:  -0.0255                                     
+REMARK   3      T13:   0.0362 T23:  -0.0257                                     
+REMARK   3    L TENSOR                                                          
+REMARK   3      L11:   3.9618 L22:   2.5662                                     
+REMARK   3      L33:   3.5301 L12:  -0.2237                                     
+REMARK   3      L13:  -2.4244 L23:  -0.7777                                     
+REMARK   3    S TENSOR                                                          
+REMARK   3      S11:  -0.1452 S12:   0.2312 S13:   0.0678                       
+REMARK   3      S21:   0.1082 S22:   0.0201 S23:   0.1702                       
+REMARK   3      S31:   0.1983 S32:  -0.3971 S33:   0.1251                       
+REMARK   3                                                                      
+REMARK   3   TLS GROUP : 2                                                      
+REMARK   3    NUMBER OF COMPONENTS GROUP : 1                                    
+REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI                         
+REMARK   3    RESIDUE RANGE :   B     2        B   122                          
+REMARK   3    ORIGIN FOR THE GROUP (A): -27.4515 -16.6414 -12.3927              
+REMARK   3    T TENSOR                                                          
+REMARK   3      T11:   0.0153 T22:   0.0305                                     
+REMARK   3      T33:   0.0110 T12:   0.0014                                     
+REMARK   3      T13:   0.0124 T23:  -0.0038                                     
+REMARK   3    L TENSOR                                                          
+REMARK   3      L11:   2.2921 L22:   2.7795                                     
+REMARK   3      L33:   6.4597 L12:   0.0122                                     
+REMARK   3      L13:   0.2226 L23:  -0.5396                                     
+REMARK   3    S TENSOR                                                          
+REMARK   3      S11:   0.0678 S12:  -0.2191 S13:   0.0982                       
+REMARK   3      S21:   0.1361 S22:   0.0490 S23:   0.0984                       
+REMARK   3      S31:  -0.1717 S32:  -0.0459 S33:  -0.1168                       
+REMARK   3                                                                      
+REMARK   3  BULK SOLVENT MODELLING.                                             
+REMARK   3   METHOD USED : MASK                                                 
+REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
+REMARK   3   VDW PROBE RADIUS   : 1.20                                          
+REMARK   3   ION PROBE RADIUS   : 0.80                                          
+REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
+REMARK   3                                                                      
+REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING   
+REMARK   3  POSITIONS                                                           
+REMARK   4                                                                      
+REMARK   4 4ZHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
+REMARK 100                                                                      
+REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-15.                  
+REMARK 100 THE DEPOSITION ID IS D_1000209256.                                   
+REMARK 200                                                                      
+REMARK 200 EXPERIMENTAL DETAILS                                                 
+REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
+REMARK 200  DATE OF DATA COLLECTION        : 21-JUL-14                          
+REMARK 200  TEMPERATURE           (KELVIN) : 100                                
+REMARK 200  PH                             : 8.5                                
+REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
+REMARK 200                                                                      
+REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
+REMARK 200  RADIATION SOURCE               : DIAMOND                            
+REMARK 200  BEAMLINE                       : I02                                
+REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
+REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
+REMARK 200  WAVELENGTH OR RANGE        (A) : 1.74                               
+REMARK 200  MONOCHROMATOR                  : SILICON CRYSTAL                    
+REMARK 200  OPTICS                         : NULL                               
+REMARK 200                                                                      
+REMARK 200  DETECTOR TYPE                  : PIXEL                              
+REMARK 200  DETECTOR MANUFACTURER          : PSI PILATUS 6M                     
+REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
+REMARK 200  DATA SCALING SOFTWARE          : AIMLESS                            
+REMARK 200                                                                      
+REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 12894                              
+REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.340                              
+REMARK 200  RESOLUTION RANGE LOW       (A) : 60.730                             
+REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
+REMARK 200                                                                      
+REMARK 200 OVERALL.                                                             
+REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.4                               
+REMARK 200  DATA REDUNDANCY                : 12.30                              
+REMARK 200  R MERGE                    (I) : 0.06600                            
+REMARK 200  R SYM                      (I) : NULL                               
+REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 23.2000                            
+REMARK 200                                                                      
+REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34                     
+REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.40                     
+REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.4                               
+REMARK 200  DATA REDUNDANCY IN SHELL       : 11.80                              
+REMARK 200  R MERGE FOR SHELL          (I) : 0.59800                            
+REMARK 200  R SYM FOR SHELL            (I) : NULL                               
+REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.200                              
+REMARK 200                                                                      
+REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
+REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL                         
+REMARK 200 SOFTWARE USED: PHASER                                                
+REMARK 200 STARTING MODEL: NULL                                                 
+REMARK 200                                                                      
+REMARK 200 REMARK: THIN PLATES, DEEP RED BROWN COLOUR DUE TO 2FE-2S IRON        
+REMARK 200  SULPHUR CLUSTER                                                     
+REMARK 280                                                                      
+REMARK 280 CRYSTAL                                                              
+REMARK 280 SOLVENT CONTENT, VS   (%): 64.33                                     
+REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45                     
+REMARK 280                                                                      
+REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M TRIS, 20 % PEG        
+REMARK 280  8000, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K       
+REMARK 290                                                                      
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
+REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2                        
+REMARK 290                                                                      
+REMARK 290      SYMOP   SYMMETRY                                                
+REMARK 290     NNNMMM   OPERATOR                                                
+REMARK 290       1555   X,Y,Z                                                   
+REMARK 290       2555   -X,-Y,Z                                                 
+REMARK 290       3555   -Y+1/2,X+1/2,Z+1/2                                      
+REMARK 290       4555   Y+1/2,-X+1/2,Z+1/2                                      
+REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/2                                     
+REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/2                                     
+REMARK 290       7555   Y,X,-Z                                                  
+REMARK 290       8555   -Y,-X,-Z                                                
+REMARK 290                                                                      
+REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
+REMARK 290           MMM -> TRANSLATION VECTOR                                  
+REMARK 290                                                                      
+REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
+REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
+REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
+REMARK 290 RELATED MOLECULES.                                                   
+REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000            
+REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       30.36500            
+REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       30.36500            
+REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       77.36500            
+REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       30.36500            
+REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       30.36500            
+REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       77.36500            
+REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       30.36500            
+REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       30.36500            
+REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       77.36500            
+REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       30.36500            
+REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       30.36500            
+REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       77.36500            
+REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
+REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
+REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
+REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000            
+REMARK 290                                                                      
+REMARK 290 REMARK: NULL                                                         
+REMARK 300                                                                      
+REMARK 300 BIOMOLECULE: 1, 2                                                    
+REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
+REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
+REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
+REMARK 300 BURIED SURFACE AREA.                                                 
+REMARK 350                                                                      
+REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
+REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
+REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
+REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
+REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
+REMARK 350                                                                      
+REMARK 350 BIOMOLECULE: 1                                                       
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
+REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 350                                                                      
+REMARK 350 BIOMOLECULE: 2                                                       
+REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
+REMARK 350 APPLY THE FOLLOWING TO CHAINS: B                                     
+REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
+REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
+REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
+REMARK 375                                                                      
+REMARK 375 SPECIAL POSITION                                                     
+REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
+REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
+REMARK 375 POSITIONS.                                                           
+REMARK 375                                                                      
+REMARK 375 ATOM RES CSSEQI                                                      
+REMARK 375      HOH B 319  LIES ON A SPECIAL POSITION.                          
+REMARK 465                                                                      
+REMARK 465 MISSING RESIDUES                                                     
+REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
+REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
+REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
+REMARK 465                                                                      
+REMARK 465   M RES C SSSEQI                                                     
+REMARK 465     MET A     1                                                      
+REMARK 465     GLU A    99                                                      
+REMARK 465     HIS A   100                                                      
+REMARK 465     HIS A   101                                                      
+REMARK 465     HIS A   102                                                      
+REMARK 465     HIS A   103                                                      
+REMARK 465     HIS A   104                                                      
+REMARK 465     HIS A   105                                                      
+REMARK 465     MET B     1                                                      
+REMARK 465     GLU B    99                                                      
+REMARK 465     HIS B   100                                                      
+REMARK 465     HIS B   101                                                      
+REMARK 465     HIS B   102                                                      
+REMARK 465     HIS B   103                                                      
+REMARK 465     HIS B   104                                                      
+REMARK 465     HIS B   105                                                      
+REMARK 470                                                                      
+REMARK 470 MISSING ATOM                                                         
+REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
+REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
+REMARK 470 I=INSERTION CODE):                                                   
+REMARK 470   M RES CSSEQI  ATOMS                                                
+REMARK 470     LEU A  98    CG   CD1  CD2                                       
+REMARK 470     LEU B  98    CG   CD1  CD2                                       
+REMARK 500                                                                      
+REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
+REMARK 500 SUBTOPIC: TORSION ANGLES                                             
+REMARK 500                                                                      
+REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
+REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
+REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
+REMARK 500                                                                      
+REMARK 500 STANDARD TABLE:                                                      
+REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
+REMARK 500                                                                      
+REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
+REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
+REMARK 500                                                                      
+REMARK 500  M RES CSSEQI        PSI       PHI                                   
+REMARK 500    SER A  39      -64.23   -146.55                                   
+REMARK 500    MET A  97      -67.17    -99.01                                   
+REMARK 500    SER B  39      -78.49   -140.11                                   
+REMARK 500    SER B  63      -12.80   -148.10                                   
+REMARK 500                                                                      
+REMARK 500 REMARK: NULL                                                         
+REMARK 620                                                                      
+REMARK 620 METAL COORDINATION                                                   
+REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
+REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
+REMARK 620                                                                      
+REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
+REMARK 620                             FES A 201  FE1                           
+REMARK 620 N RES CSSEQI ATOM                                                    
+REMARK 620 1 CYS A  40   SG                                                     
+REMARK 620 2 FES A 201   S1  124.8                                              
+REMARK 620 3 FES A 201   S2  100.1  99.4                                        
+REMARK 620 4 CYS A  45   SG  105.3 110.0 117.8                                  
+REMARK 620 N                    1     2     3                                   
+REMARK 620                                                                      
+REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
+REMARK 620                             FES A 201  FE2                           
+REMARK 620 N RES CSSEQI ATOM                                                    
+REMARK 620 1 CYS A  48   SG                                                     
+REMARK 620 2 FES A 201   S1  114.4                                              
+REMARK 620 3 FES A 201   S2  108.9 101.7                                        
+REMARK 620 4 CYS A  78   SG  105.9 122.0 102.7                                  
+REMARK 620 N                    1     2     3                                   
+REMARK 620                                                                      
+REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
+REMARK 620                             FES B 201  FE1                           
+REMARK 620 N RES CSSEQI ATOM                                                    
+REMARK 620 1 CYS B  40   SG                                                     
+REMARK 620 2 FES B 201   S1  119.9                                              
+REMARK 620 3 FES B 201   S2  102.0  97.8                                        
+REMARK 620 4 CYS B  45   SG  109.5 108.1 119.7                                  
+REMARK 620 N                    1     2     3                                   
+REMARK 620                                                                      
+REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
+REMARK 620                             FES B 201  FE2                           
+REMARK 620 N RES CSSEQI ATOM                                                    
+REMARK 620 1 CYS B  48   SG                                                     
+REMARK 620 2 FES B 201   S1  111.1                                              
+REMARK 620 3 FES B 201   S2  115.5  99.1                                        
+REMARK 620 4 CYS B  78   SG  110.9 117.2 102.5                                  
+REMARK 620 N                    1     2     3                                   
+REMARK 800                                                                      
+REMARK 800 SITE                                                                 
+REMARK 800 SITE_IDENTIFIER: AC1                                                 
+REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
+REMARK 800 SITE_DESCRIPTION: binding site for residue FES A 201                 
+REMARK 800                                                                      
+REMARK 800 SITE_IDENTIFIER: AC2                                                 
+REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
+REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202                  
+REMARK 800                                                                      
+REMARK 800 SITE_IDENTIFIER: AC3                                                 
+REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
+REMARK 800 SITE_DESCRIPTION: binding site for residue FES B 201                 
+REMARK 800                                                                      
+REMARK 800 SITE_IDENTIFIER: AC4                                                 
+REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
+REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 202                  
+DBREF  4ZHO A    1    94  UNP    P16972   FER2_ARATH      52    145             
+DBREF  4ZHO B    1    94  UNP    P16972   FER2_ARATH      52    145             
+SEQADV 4ZHO ALA A   95  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO ILE A   96  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO MET A   97  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO LEU A   98  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO GLU A   99  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS A  100  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS A  101  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS A  102  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS A  103  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS A  104  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS A  105  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO ALA B   95  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO ILE B   96  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO MET B   97  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO LEU B   98  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO GLU B   99  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS B  100  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS B  101  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS B  102  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS B  103  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS B  104  UNP  P16972              EXPRESSION TAG                 
+SEQADV 4ZHO HIS B  105  UNP  P16972              EXPRESSION TAG                 
+SEQRES   1 A  105  MET ALA THR TYR LYS VAL LYS PHE ILE THR PRO GLU GLY          
+SEQRES   2 A  105  GLU LEU GLU VAL GLU CYS ASP ASP ASP VAL TYR VAL LEU          
+SEQRES   3 A  105  ASP ALA ALA GLU GLU ALA GLY ILE ASP LEU PRO TYR SER          
+SEQRES   4 A  105  CYS ARG ALA GLY SER CYS SER SER CYS ALA GLY LYS VAL          
+SEQRES   5 A  105  VAL SER GLY SER VAL ASP GLN SER ASP GLN SER PHE LEU          
+SEQRES   6 A  105  ASP ASP GLU GLN ILE GLY GLU GLY PHE VAL LEU THR CYS          
+SEQRES   7 A  105  ALA ALA TYR PRO THR SER ASP VAL THR ILE GLU THR HIS          
+SEQRES   8 A  105  LYS GLU GLU ALA ILE MET LEU GLU HIS HIS HIS HIS HIS          
+SEQRES   9 A  105  HIS                                                          
+SEQRES   1 B  105  MET ALA THR TYR LYS VAL LYS PHE ILE THR PRO GLU GLY          
+SEQRES   2 B  105  GLU LEU GLU VAL GLU CYS ASP ASP ASP VAL TYR VAL LEU          
+SEQRES   3 B  105  ASP ALA ALA GLU GLU ALA GLY ILE ASP LEU PRO TYR SER          
+SEQRES   4 B  105  CYS ARG ALA GLY SER CYS SER SER CYS ALA GLY LYS VAL          
+SEQRES   5 B  105  VAL SER GLY SER VAL ASP GLN SER ASP GLN SER PHE LEU          
+SEQRES   6 B  105  ASP ASP GLU GLN ILE GLY GLU GLY PHE VAL LEU THR CYS          
+SEQRES   7 B  105  ALA ALA TYR PRO THR SER ASP VAL THR ILE GLU THR HIS          
+SEQRES   8 B  105  LYS GLU GLU ALA ILE MET LEU GLU HIS HIS HIS HIS HIS          
+SEQRES   9 B  105  HIS                                                          
+HET    FES  A 201       4                                                       
+HET     CL  A 202       1                                                       
+HET    FES  B 201       4                                                       
+HET     CL  B 202       1                                                       
+HETNAM     FES FE2/S2 (INORGANIC) CLUSTER                                       
+HETNAM      CL CHLORIDE ION                                                     
+FORMUL   3  FES    2(FE2 S2)                                                    
+FORMUL   4   CL    2(CL 1-)                                                     
+FORMUL   7  HOH   *38(H2 O)                                                     
+HELIX    1 AA1 TYR A   24  ALA A   32  1                                   9    
+HELIX    2 AA2 ASP A   66  GLU A   72  1                                   7    
+HELIX    3 AA3 CYS A   78  ALA A   80  5                                   3    
+HELIX    4 AA5 TYR B   24  ALA B   32  1                                   9    
+HELIX    5 AA6 ASP B   66  GLU B   72  1                                   7    
+HELIX    6 AA7 CYS B   78  ALA B   80  5                                   3    
+HELIX    7 AA8 LYS B   92  MET B   97  5                                   6    
+SHEET    1 AA1 5 GLU A  14  ASP A  20  0                                        
+SHEET    2 AA1 5 THR A   3  ILE A   9 -1  N  PHE A   8   O  LEU A  15           
+SHEET    3 AA1 5 VAL A  86  GLU A  89  1  O  ILE A  88   N  LYS A   7           
+SHEET    4 AA1 5 ALA A  49  SER A  54 -1  N  SER A  54   O  THR A  87           
+SHEET    5 AA1 5 PHE A  74  LEU A  76 -1  O  VAL A  75   N  GLY A  50           
+SHEET    1 AA2 2 VAL A  57  ASP A  58  0                                        
+SHEET    2 AA2 2 TYR A  81  PRO A  82 -1  O  TYR A  81   N  ASP A  58           
+SHEET    1 AA3 5 GLY B  13  ASP B  20  0                                        
+SHEET    2 AA3 5 THR B   3  THR B  10 -1  N  PHE B   8   O  LEU B  15           
+SHEET    3 AA3 5 VAL B  86  GLU B  89  1  O  ILE B  88   N  LYS B   7           
+SHEET    4 AA3 5 ALA B  49  SER B  54 -1  N  LYS B  51   O  GLU B  89           
+SHEET    5 AA3 5 PHE B  74  LEU B  76 -1  O  VAL B  75   N  GLY B  50           
+SHEET    1 AA4 2 VAL B  57  ASP B  58  0                                        
+SHEET    2 AA4 2 TYR B  81  PRO B  82 -1  O  TYR B  81   N  ASP B  58           
+LINK         SG  CYS A  40                FE1  FES A 201     1555   1555  2.33  
+LINK         SG  CYS A  45                FE1  FES A 201     1555   1555  2.28  
+LINK         SG  CYS A  48                FE2  FES A 201     1555   1555  2.28  
+LINK         SG  CYS A  78                FE2  FES A 201     1555   1555  2.34  
+LINK         SG  CYS B  40                FE1  FES B 201     1555   1555  2.22  
+LINK         SG  CYS B  45                FE1  FES B 201     1555   1555  2.25  
+LINK         SG  CYS B  48                FE2  FES B 201     1555   1555  2.18  
+LINK         SG  CYS B  78                FE2  FES B 201     1555   1555  2.36  
+SITE     1 AC1  8 SER A  39  CYS A  40  ARG A  41  GLY A  43                    
+SITE     2 AC1  8 SER A  44  CYS A  45  CYS A  48  CYS A  78                    
+SITE     1 AC2  2 SER A  84  ASP A  85                                          
+SITE     1 AC3  8 SER B  39  CYS B  40  ARG B  41  GLY B  43                    
+SITE     2 AC3  8 SER B  44  CYS B  45  CYS B  48  CYS B  78                    
+SITE     1 AC4  2 SER B  84  ASP B  85                                          
+CRYST1   60.730   60.730  154.730  90.00  90.00  90.00 P 42 21 2    16          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.016466  0.000000  0.000000        0.00000                         
+SCALE2      0.000000  0.016466  0.000000        0.00000                         
+SCALE3      0.000000  0.000000  0.006463        0.00000                         
+ATOM      1  N   ALA A   2      -1.257 -15.807 -48.124  1.00 50.77           N  
+ANISOU    1  N   ALA A   2     7787   5804   5698   -219   1819   -481       N  
+ATOM      2  CA  ALA A   2      -1.523 -14.339 -48.197  1.00 50.70           C  
+ANISOU    2  CA  ALA A   2     7568   6034   5660   -183   1548   -344       C  
+ATOM      3  C   ALA A   2      -1.438 -13.722 -46.830  1.00 45.70           C  
+ANISOU    3  C   ALA A   2     6785   5347   5230    -97   1396   -189       C  
+ATOM      4  O   ALA A   2      -1.809 -14.345 -45.825  1.00 44.98           O  
+ANISOU    4  O   ALA A   2     6732   5134   5221   -136   1414   -240       O  
+ATOM      5  CB  ALA A   2      -2.903 -14.040 -48.848  1.00 48.96           C  
+ANISOU    5  CB  ALA A   2     7316   6077   5207   -370   1390   -508       C  
+ATOM      6  N   THR A   3      -1.069 -12.455 -46.833  1.00 45.54           N  
+ANISOU    6  N   THR A   3     6600   5431   5271     -1   1249    -16       N  
+ATOM      7  CA  THR A   3      -0.949 -11.641 -45.631  1.00 47.35           C  
+ANISOU    7  CA  THR A   3     6681   5636   5674     60   1092    109       C  
+ATOM      8  C   THR A   3      -1.689 -10.384 -45.941  1.00 43.11           C  
+ANISOU    8  C   THR A   3     6022   5274   5083     31    915    145       C  
+ATOM      9  O   THR A   3      -1.531  -9.803 -47.012  1.00 41.92           O  
+ANISOU    9  O   THR A   3     5843   5236   4848     63    924    210       O  
+ATOM     10  CB  THR A   3       0.543 -11.321 -45.328  1.00 50.05           C  
+ANISOU   10  CB  THR A   3     6935   5888   6195    216   1141    301       C  
+ATOM     11  OG1 THR A   3       1.229 -12.551 -45.036  1.00 50.95           O  
+ANISOU   11  OG1 THR A   3     7151   5846   6362    283   1328    306       O  
+ATOM     12  CG2 THR A   3       0.673 -10.438 -44.115  1.00 54.46           C  
+ANISOU   12  CG2 THR A   3     7341   6448   6902    242    968    390       C  
+ATOM     13  N   TYR A   4      -2.484  -9.944 -44.989  1.00 46.99           N  
+ANISOU   13  N   TYR A   4     6443   5784   5625     -9    776    123       N  
+ATOM     14  CA  TYR A   4      -3.347  -8.768 -45.177  1.00 48.43           C  
+ANISOU   14  CA  TYR A   4     6510   6116   5775    -19    632    167       C  
+ATOM     15  C   TYR A   4      -3.023  -7.694 -44.144  1.00 47.22           C  
+ANISOU   15  C   TYR A   4     6246   5881   5813     46    540    272       C  
+ATOM     16  O   TYR A   4      -2.521  -7.988 -43.069  1.00 48.33           O  
+ANISOU   16  O   TYR A   4     6396   5904   6063     58    537    263       O  
+ATOM     17  CB  TYR A   4      -4.801  -9.196 -45.059  1.00 47.01           C  
+ANISOU   17  CB  TYR A   4     6341   6049   5468   -146    570     20       C  
+ATOM     18  CG  TYR A   4      -5.208 -10.134 -46.157  1.00 43.84           C  
+ANISOU   18  CG  TYR A   4     6035   5763   4857   -258    645   -122       C  
+ATOM     19  CD1 TYR A   4      -5.280  -9.700 -47.461  1.00 48.21           C  
+ANISOU   19  CD1 TYR A   4     6559   6515   5243   -243    630    -80       C  
+ATOM     20  CD2 TYR A   4      -5.473 -11.470 -45.898  1.00 48.38           C  
+ANISOU   20  CD2 TYR A   4     6743   6241   5397   -383    752   -303       C  
+ATOM     21  CE1 TYR A   4      -5.629 -10.561 -48.480  1.00 48.93           C  
+ANISOU   21  CE1 TYR A   4     6746   6739   5104   -368    694   -244       C  
+ATOM     22  CE2 TYR A   4      -5.802 -12.362 -46.923  1.00 48.52           C  
+ANISOU   22  CE2 TYR A   4     6868   6342   5221   -522    844   -480       C  
+ATOM     23  CZ  TYR A   4      -5.914 -11.892 -48.199  1.00 48.26           C  
+ANISOU   23  CZ  TYR A   4     6798   6543   4992   -526    799   -466       C  
+ATOM     24  OH  TYR A   4      -6.226 -12.778 -49.220  1.00 52.35           O  
+ANISOU   24  OH  TYR A   4     7434   7172   5284   -686    885   -675       O  
+ATOM     25  N   LYS A   5      -3.307  -6.453 -44.489  1.00 47.90           N  
+ANISOU   25  N   LYS A   5     6234   6036   5930     90    478    373       N  
+ATOM     26  CA  LYS A   5      -3.126  -5.320 -43.582  1.00 49.46           C  
+ANISOU   26  CA  LYS A   5     6343   6138   6309    126    414    439       C  
+ATOM     27  C   LYS A   5      -4.415  -5.114 -42.819  1.00 44.72           C  
+ANISOU   27  C   LYS A   5     5725   5576   5688     87    334    362       C  
+ATOM     28  O   LYS A   5      -5.464  -4.904 -43.423  1.00 45.76           O  
+ANISOU   28  O   LYS A   5     5820   5852   5714     87    308    374       O  
+ATOM     29  CB  LYS A   5      -2.776  -4.038 -44.357  1.00 51.93           C  
+ANISOU   29  CB  LYS A   5     6573   6454   6702    205    443    602       C  
+ATOM     30  CG  LYS A   5      -1.497  -4.126 -45.113  1.00 62.94           C  
+ANISOU   30  CG  LYS A   5     7967   7811   8137    249    542    698       C  
+ATOM     31  CD  LYS A   5      -0.351  -4.665 -44.240  1.00 71.74           C  
+ANISOU   31  CD  LYS A   5     9078   8803   9377    228    553    662       C  
+ATOM     32  CE  LYS A   5      -0.083  -3.798 -43.025  1.00 78.38           C  
+ANISOU   32  CE  LYS A   5     9836   9541  10403    192    473    648       C  
+ATOM     33  NZ  LYS A   5       0.491  -2.513 -43.496  1.00 87.36           N  
+ANISOU   33  NZ  LYS A   5    10881  10609  11701    215    524    774       N  
+ATOM     34  N   VAL A   6      -4.356  -5.236 -41.505  1.00 40.33           N  
+ANISOU   34  N   VAL A   6     5186   4922   5213     58    297    290       N  
+ATOM     35  CA  VAL A   6      -5.506  -4.978 -40.686  1.00 43.48           C  
+ANISOU   35  CA  VAL A   6     5572   5340   5608     33    246    224       C  
+ATOM     36  C   VAL A   6      -5.286  -3.624 -40.015  1.00 44.26           C  
+ANISOU   36  C   VAL A   6     5616   5334   5865     73    225    265       C  
+ATOM     37  O   VAL A   6      -4.317  -3.413 -39.286  1.00 45.54           O  
+ANISOU   37  O   VAL A   6     5782   5395   6125     57    211    245       O  
+ATOM     38  CB  VAL A   6      -5.704  -6.072 -39.614  1.00 47.03           C  
+ANISOU   38  CB  VAL A   6     6100   5753   6016    -24    246    110       C  
+ATOM     39  CG1 VAL A   6      -6.982  -5.808 -38.849  1.00 45.34           C  
+ANISOU   39  CG1 VAL A   6     5866   5571   5789    -46    216     50       C  
+ATOM     40  CG2 VAL A   6      -5.764  -7.451 -40.254  1.00 46.02           C  
+ANISOU   40  CG2 VAL A   6     6052   5664   5769    -78    315     53       C  
+ATOM     41  N   LYS A   7      -6.163  -2.682 -40.330  1.00 45.38           N  
+ANISOU   41  N   LYS A   7     5700   5508   6034    123    235    327       N  
+ATOM     42  CA  LYS A   7      -6.143  -1.373 -39.740  1.00 45.98           C  
+ANISOU   42  CA  LYS A   7     5748   5450   6273    160    263    351       C  
+ATOM     43  C   LYS A   7      -7.143  -1.363 -38.592  1.00 47.81           C  
+ANISOU   43  C   LYS A   7     6003   5668   6491    143    248    245       C  
+ATOM     44  O   LYS A   7      -8.347  -1.536 -38.787  1.00 51.78           O  
+ANISOU   44  O   LYS A   7     6468   6287   6918    173    249    263       O  
+ATOM     45  CB  LYS A   7      -6.506  -0.347 -40.788  1.00 48.29           C  
+ANISOU   45  CB  LYS A   7     5968   5763   6617    264    329    520       C  
+ATOM     46  CG  LYS A   7      -6.637   1.070 -40.268  1.00 58.39           C  
+ANISOU   46  CG  LYS A   7     7234   6859   8090    316    413    556       C  
+ATOM     47  CD  LYS A   7      -6.631   2.026 -41.447  1.00 68.64           C  
+ANISOU   47  CD  LYS A   7     8467   8148   9461    441    515    776       C  
+ATOM     48  CE  LYS A   7      -6.930   3.448 -41.018  1.00 82.52           C  
+ANISOU   48  CE  LYS A   7    10225   9693  11435    515    651    833       C  
+ATOM     49  NZ  LYS A   7      -6.213   4.399 -41.926  1.00 90.34           N  
+ANISOU   49  NZ  LYS A   7    11188  10561  12575    587    785   1022       N  
+ATOM     50  N   PHE A   8      -6.640  -1.148 -37.392  1.00 43.94           N  
+ANISOU   50  N   PHE A   8     5567   5061   6068     93    233    136       N  
+ATOM     51  CA  PHE A   8      -7.513  -1.002 -36.238  1.00 50.30           C  
+ANISOU   51  CA  PHE A   8     6412   5840   6859     87    244     34       C  
+ATOM     52  C   PHE A   8      -7.808   0.440 -35.906  1.00 44.05           C  
+ANISOU   52  C   PHE A   8     5618   4900   6218    131    331     33       C  
+ATOM     53  O   PHE A   8      -6.905   1.228 -35.663  1.00 48.85           O  
+ANISOU   53  O   PHE A   8     6245   5366   6948     88    353     -5       O  
+ATOM     54  CB  PHE A   8      -6.843  -1.646 -35.018  1.00 45.89           C  
+ANISOU   54  CB  PHE A   8     5927   5267   6239     10    184    -93       C  
+ATOM     55  CG  PHE A   8      -6.679  -3.122 -35.144  1.00 46.40           C  
+ANISOU   55  CG  PHE A   8     6019   5437   6174    -10    148    -85       C  
+ATOM     56  CD1 PHE A   8      -7.769  -3.967 -35.038  1.00 48.26           C  
+ANISOU   56  CD1 PHE A   8     6277   5749   6311    -14    173   -106       C  
+ATOM     57  CD2 PHE A   8      -5.438  -3.668 -35.354  1.00 44.91           C  
+ANISOU   57  CD2 PHE A   8     5828   5253   5981    -27    113    -54       C  
+ATOM     58  CE1 PHE A   8      -7.601  -5.339 -35.131  1.00 47.89           C  
+ANISOU   58  CE1 PHE A   8     6276   5748   6170    -46    182   -111       C  
+ATOM     59  CE2 PHE A   8      -5.279  -5.027 -35.445  1.00 45.32           C  
+ANISOU   59  CE2 PHE A   8     5923   5360   5935    -28    125    -39       C  
+ATOM     60  CZ  PHE A   8      -6.356  -5.857 -35.342  1.00 47.01           C  
+ANISOU   60  CZ  PHE A   8     6184   5615   6059    -43    168    -74       C  
+ATOM     61  N   ILE A   9      -9.069   0.763 -35.795  1.00 45.19           N  
+ANISOU   61  N   ILE A   9     5739   5067   6363    208    395     63       N  
+ATOM     62  CA  ILE A   9      -9.459   2.100 -35.309  1.00 51.68           C  
+ANISOU   62  CA  ILE A   9     6584   5712   7339    270    525     51       C  
+ATOM     63  C   ILE A   9      -9.826   1.880 -33.879  1.00 50.92           C  
+ANISOU   63  C   ILE A   9     6580   5587   7179    217    529   -126       C  
+ATOM     64  O   ILE A   9     -10.824   1.229 -33.599  1.00 53.51           O  
+ANISOU   64  O   ILE A   9     6889   6036   7407    248    527   -124       O  
+ATOM     65  CB  ILE A   9     -10.635   2.697 -36.124  1.00 55.53           C  
+ANISOU   65  CB  ILE A   9     6967   6250   7879    433    624    240       C  
+ATOM     66  CG1 ILE A   9     -10.204   2.918 -37.592  1.00 55.29           C  
+ANISOU   66  CG1 ILE A   9     6852   6282   7873    497    619    438       C  
+ATOM     67  CG2 ILE A   9     -11.137   4.018 -35.502  1.00 55.96           C  
+ANISOU   67  CG2 ILE A   9     7065   6086   8109    523    808    232       C  
+ATOM     68  CD1 ILE A   9     -11.385   2.981 -38.527  1.00 58.25           C  
+ANISOU   68  CD1 ILE A   9     7085   6859   8188    645    639    641       C  
+ATOM     69  N   THR A  10      -8.967   2.329 -32.980  1.00 50.67           N  
+ANISOU   69  N   THR A  10     6641   5425   7186    121    526   -284       N  
+ATOM     70  CA  THR A  10      -9.185   2.107 -31.561  1.00 51.69           C  
+ANISOU   70  CA  THR A  10     6873   5558   7208     65    520   -464       C  
+ATOM     71  C   THR A  10      -9.612   3.432 -30.915  1.00 50.65           C  
+ANISOU   71  C   THR A  10     6822   5218   7204     89    689   -568       C  
+ATOM     72  O   THR A  10      -9.544   4.466 -31.525  1.00 57.26           O  
+ANISOU   72  O   THR A  10     7639   5887   8228    134    806   -501       O  
+ATOM     73  CB  THR A  10      -7.930   1.531 -30.864  1.00 50.80           C  
+ANISOU   73  CB  THR A  10     6804   5512   6986    -68    378   -588       C  
+ATOM     74  OG1 THR A  10      -6.968   2.554 -30.671  1.00 53.43           O  
+ANISOU   74  OG1 THR A  10     7157   5704   7440   -168    390   -696       O  
+ATOM     75  CG2 THR A  10      -7.278   0.462 -31.693  1.00 50.38           C  
+ANISOU   75  CG2 THR A  10     6674   5593   6874    -73    264   -466       C  
+ATOM     76  N   PRO A  11     -10.106   3.393 -29.679  1.00 56.03           N  
+ANISOU   76  N   PRO A  11     7607   5897   7785     72    733   -722       N  
+ATOM     77  CA  PRO A  11     -10.427   4.652 -28.979  1.00 58.93           C  
+ANISOU   77  CA  PRO A  11     8085   6039   8264     79    922   -863       C  
+ATOM     78  C   PRO A  11      -9.259   5.590 -28.772  1.00 63.22           C  
+ANISOU   78  C   PRO A  11     8697   6403   8918    -73    935  -1031       C  
+ATOM     79  O   PRO A  11      -9.508   6.756 -28.521  1.00 69.60           O  
+ANISOU   79  O   PRO A  11     9594   6966   9884    -65   1137  -1123       O  
+ATOM     80  CB  PRO A  11     -10.886   4.178 -27.593  1.00 59.38           C  
+ANISOU   80  CB  PRO A  11     8256   6185   8120     51    924  -1030       C  
+ATOM     81  CG  PRO A  11     -11.306   2.750 -27.777  1.00 55.35           C  
+ANISOU   81  CG  PRO A  11     7663   5915   7451     96    802   -896       C  
+ATOM     82  CD  PRO A  11     -10.443   2.207 -28.868  1.00 52.67           C  
+ANISOU   82  CD  PRO A  11     7215   5657   7140     56    649   -769       C  
+ATOM     83  N   GLU A  12      -8.030   5.041 -28.776  1.00 70.08           N  
+ANISOU   83  N   GLU A  12     9526   7398   9704   -217    738  -1080       N  
+ATOM     84  CA  GLU A  12      -6.732   5.771 -28.699  1.00 69.59           C  
+ANISOU   84  CA  GLU A  12     9470   7225   9747   -402    705  -1227       C  
+ATOM     85  C   GLU A  12      -6.252   6.249 -30.096  1.00 71.32           C  
+ANISOU   85  C   GLU A  12     9578   7319  10199   -369    757  -1033       C  
+ATOM     86  O   GLU A  12      -5.575   7.279 -30.200  1.00 82.47           O  
+ANISOU   86  O   GLU A  12    11009   8520  11805   -484    854  -1123       O  
+ATOM     87  CB  GLU A  12      -5.618   4.877 -28.105  1.00 80.51           C  
+ANISOU   87  CB  GLU A  12    10809   8855  10925   -546    460  -1320       C  
+ATOM     88  CG  GLU A  12      -5.569   4.624 -26.578  1.00 89.15           C  
+ANISOU   88  CG  GLU A  12    12010  10093  11769   -643    381  -1555       C  
+ATOM     89  CD  GLU A  12      -4.271   3.871 -26.137  1.00 96.47           C  
+ANISOU   89  CD  GLU A  12    12846  11289  12519   -771    133  -1597       C  
+ATOM     90  OE1 GLU A  12      -3.440   4.458 -25.401  1.00 86.42           O  
+ANISOU   90  OE1 GLU A  12    11584  10049  11202   -968     64  -1827       O  
+ATOM     91  OE2 GLU A  12      -4.044   2.692 -26.542  1.00 87.89           O  
+ANISOU   91  OE2 GLU A  12    11665  10388  11340   -678     12  -1398       O  
+ATOM     92  N   GLY A  13      -6.566   5.500 -31.160  1.00 63.49           N  
+ANISOU   92  N   GLY A  13     8479   6460   9184   -227    703   -780       N  
+ATOM     93  CA  GLY A  13      -6.219   5.913 -32.504  1.00 59.26           C  
+ANISOU   93  CA  GLY A  13     7850   5841   8826   -167    764   -575       C  
+ATOM     94  C   GLY A  13      -6.111   4.770 -33.479  1.00 56.21           C  
+ANISOU   94  C   GLY A  13     7353   5681   8322    -92    628   -378       C  
+ATOM     95  O   GLY A  13      -6.534   3.652 -33.197  1.00 53.58           O  
+ANISOU   95  O   GLY A  13     7018   5544   7795    -65    517   -379       O  
+ATOM     96  N   GLU A  14      -5.519   5.057 -34.631  1.00 54.33           N  
+ANISOU   96  N   GLU A  14     7036   5399   8206    -65    661   -215       N  
+ATOM     97  CA  GLU A  14      -5.492   4.115 -35.751  1.00 60.06           C  
+ANISOU   97  CA  GLU A  14     7674   6319   8826     19    577    -23       C  
+ATOM     98  C   GLU A  14      -4.126   3.540 -35.940  1.00 51.22           C  
+ANISOU   98  C   GLU A  14     6504   5271   7684    -88    464    -38       C  
+ATOM     99  O   GLU A  14      -3.198   4.277 -36.050  1.00 52.79           O  
+ANISOU   99  O   GLU A  14     6674   5338   8045   -172    512    -55       O  
+ATOM    100  CB  GLU A  14      -5.953   4.814 -37.053  1.00 67.15           C  
+ANISOU  100  CB  GLU A  14     8513   7162   9837    174    715    218       C  
+ATOM    101  CG  GLU A  14      -7.367   5.360 -36.842  1.00 82.24           C  
+ANISOU  101  CG  GLU A  14    10442   9031  11772    314    834    268       C  
+ATOM    102  CD  GLU A  14      -7.938   6.250 -37.944  1.00 92.51           C  
+ANISOU  102  CD  GLU A  14    11677  10275  13196    506    998    534       C  
+ATOM    103  OE1 GLU A  14      -7.274   6.424 -38.992  1.00104.38           O  
+ANISOU  103  OE1 GLU A  14    13129  11783  14748    536   1022    696       O  
+ATOM    104  OE2 GLU A  14      -9.080   6.772 -37.742  1.00 86.19           O  
+ANISOU  104  OE2 GLU A  14    10870   9437  12438    645   1116    601       O  
+ATOM    105  N   LEU A  15      -4.066   2.220 -36.076  1.00 51.18           N  
+ANISOU  105  N   LEU A  15     6481   5467   7497    -72    343    -11       N  
+ATOM    106  CA  LEU A  15      -2.856   1.402 -36.095  1.00 54.47           C  
+ANISOU  106  CA  LEU A  15     6850   5982   7861   -141    239    -15       C  
+ATOM    107  C   LEU A  15      -3.099   0.276 -37.078  1.00 53.30           C  
+ANISOU  107  C   LEU A  15     6690   5980   7581    -52    221    115       C  
+ATOM    108  O   LEU A  15      -4.183  -0.290 -37.098  1.00 48.80           O  
+ANISOU  108  O   LEU A  15     6160   5493   6889      1    217    115       O  
+ATOM    109  CB  LEU A  15      -2.708   0.632 -34.773  1.00 53.82           C  
+ANISOU  109  CB  LEU A  15     6808   6004   7634   -208    122   -164       C  
+ATOM    110  CG  LEU A  15      -2.570   1.415 -33.509  1.00 64.22           C  
+ANISOU  110  CG  LEU A  15     8165   7251   8981   -319    102   -355       C  
+ATOM    111  CD1 LEU A  15      -2.755   0.471 -32.348  1.00 68.91           C  
+ANISOU  111  CD1 LEU A  15     8813   8000   9367   -328      0   -448       C  
+ATOM    112  CD2 LEU A  15      -1.203   2.057 -33.474  1.00 66.88           C  
+ANISOU  112  CD2 LEU A  15     8412   7542   9455   -454     71   -403       C  
+ATOM    113  N   GLU A  16      -2.062  -0.144 -37.776  1.00 49.83           N  
+ANISOU  113  N   GLU A  16     6195   5579   7157    -55    214    200       N  
+ATOM    114  CA  GLU A  16      -2.191  -1.180 -38.784  1.00 52.00           C  
+ANISOU  114  CA  GLU A  16     6480   5971   7306     14    227    299       C  
+ATOM    115  C   GLU A  16      -1.165  -2.260 -38.528  1.00 44.99           C  
+ANISOU  115  C   GLU A  16     5581   5146   6365     -5    183    291       C  
+ATOM    116  O   GLU A  16      -0.027  -1.953 -38.247  1.00 41.15           O  
+ANISOU  116  O   GLU A  16     5017   4632   5983    -49    162    300       O  
+ATOM    117  CB  GLU A  16      -1.924  -0.519 -40.111  1.00 56.47           C  
+ANISOU  117  CB  GLU A  16     6996   6506   7952     73    320    454       C  
+ATOM    118  CG  GLU A  16      -2.598  -1.111 -41.299  1.00 64.79           C  
+ANISOU  118  CG  GLU A  16     8072   7693   8851    152    352    546       C  
+ATOM    119  CD  GLU A  16      -2.299  -0.276 -42.542  1.00 77.28           C  
+ANISOU  119  CD  GLU A  16     9604   9258  10500    229    453    725       C  
+ATOM    120  OE1 GLU A  16      -1.932  -0.864 -43.609  1.00 78.06           O  
+ANISOU  120  OE1 GLU A  16     9708   9456  10491    269    492    807       O  
+ATOM    121  OE2 GLU A  16      -2.392   0.977 -42.427  1.00 67.17           O  
+ANISOU  121  OE2 GLU A  16     8290   7846   9385    251    517    784       O  
+ATOM    122  N   VAL A  17      -1.538  -3.520 -38.672  1.00 44.95           N  
+ANISOU  122  N   VAL A  17     5642   5223   6212     27    187    284       N  
+ATOM    123  CA  VAL A  17      -0.578  -4.609 -38.466  1.00 43.94           C  
+ANISOU  123  CA  VAL A  17     5513   5132   6048     46    189    310       C  
+ATOM    124  C   VAL A  17      -0.754  -5.509 -39.643  1.00 44.55           C  
+ANISOU  124  C   VAL A  17     5652   5239   6033     92    285    360       C  
+ATOM    125  O   VAL A  17      -1.732  -5.387 -40.374  1.00 43.66           O  
+ANISOU  125  O   VAL A  17     5577   5162   5847     87    308    346       O  
+ATOM    126  CB  VAL A  17      -0.860  -5.372 -37.157  1.00 48.00           C  
+ANISOU  126  CB  VAL A  17     6081   5682   6472     37    134    232       C  
+ATOM    127  CG1 VAL A  17      -0.799  -4.395 -35.985  1.00 48.79           C  
+ANISOU  127  CG1 VAL A  17     6138   5776   6622    -25     37    146       C  
+ATOM    128  CG2 VAL A  17      -2.229  -6.014 -37.217  1.00 46.07           C  
+ANISOU  128  CG2 VAL A  17     5942   5449   6111     34    172    170       C  
+ATOM    129  N   GLU A  18       0.203  -6.379 -39.858  1.00 39.17           N  
+ANISOU  129  N   GLU A  18     4974   4558   5351    139    347    420       N  
+ATOM    130  CA  GLU A  18       0.027  -7.446 -40.834  1.00 45.65           C  
+ANISOU  130  CA  GLU A  18     5895   5385   6065    169    468    423       C  
+ATOM    131  C   GLU A  18      -0.549  -8.660 -40.120  1.00 42.91           C  
+ANISOU  131  C   GLU A  18     5658   5017   5628    157    500    342       C  
+ATOM    132  O   GLU A  18      -0.225  -8.908 -38.983  1.00 50.61           O  
+ANISOU  132  O   GLU A  18     6614   5981   6632    182    459    356       O  
+ATOM    133  CB  GLU A  18       1.373  -7.869 -41.404  1.00 49.05           C  
+ANISOU  133  CB  GLU A  18     6290   5791   6555    246    574    536       C  
+ATOM    134  CG  GLU A  18       1.849  -7.008 -42.535  1.00 63.96           C  
+ANISOU  134  CG  GLU A  18     8110   7691   8497    264    618    626       C  
+ATOM    135  CD  GLU A  18       3.316  -7.261 -42.867  1.00 75.06           C  
+ANISOU  135  CD  GLU A  18     9436   9075  10006    344    719    757       C  
+ATOM    136  OE1 GLU A  18       3.833  -8.337 -42.508  1.00 68.87           O  
+ANISOU  136  OE1 GLU A  18     8682   8270   9214    408    790    779       O  
+ATOM    137  OE2 GLU A  18       3.953  -6.347 -43.437  1.00 86.26           O  
+ANISOU  137  OE2 GLU A  18    10749  10492  11532    351    741    855       O  
+ATOM    138  N   CYS A  19      -1.403  -9.397 -40.824  1.00 42.18           N  
+ANISOU  138  N   CYS A  19     5675   4930   5420    110    580    258       N  
+ATOM    139  CA  CYS A  19      -2.100 -10.522 -40.319  1.00 42.40           C  
+ANISOU  139  CA  CYS A  19     5816   4913   5379     67    646    167       C  
+ATOM    140  C   CYS A  19      -2.196 -11.521 -41.439  1.00 43.87           C  
+ANISOU  140  C   CYS A  19     6123   5068   5477     29    804     99       C  
+ATOM    141  O   CYS A  19      -2.743 -11.212 -42.516  1.00 43.45           O  
+ANISOU  141  O   CYS A  19     6070   5112   5326    -37    790     39       O  
+ATOM    142  CB  CYS A  19      -3.524 -10.140 -39.826  1.00 45.74           C  
+ANISOU  142  CB  CYS A  19     6229   5397   5751    -23    551     67       C  
+ATOM    143  SG  CYS A  19      -4.342 -11.539 -39.028  1.00 48.02           S  
+ANISOU  143  SG  CYS A  19     6646   5607   5990    -86    658    -31       S  
+ATOM    144  N   ASP A  20      -1.642 -12.721 -41.204  1.00 45.23           N  
+ANISOU  144  N   ASP A  20     6401   5109   5674     79    970    112       N  
+ATOM    145  CA  ASP A  20      -1.719 -13.795 -42.164  1.00 47.07           C  
+ANISOU  145  CA  ASP A  20     6786   5262   5833     28   1168     13       C  
+ATOM    146  C   ASP A  20      -3.181 -14.220 -42.331  1.00 49.54           C  
+ANISOU  146  C   ASP A  20     7175   5613   6035   -157   1166   -185       C  
+ATOM    147  O   ASP A  20      -4.027 -14.046 -41.400  1.00 46.05           O  
+ANISOU  147  O   ASP A  20     6690   5197   5609   -209   1069   -212       O  
+ATOM    148  CB  ASP A  20      -0.895 -14.979 -41.694  1.00 49.71           C  
+ANISOU  148  CB  ASP A  20     7224   5411   6252    141   1380     87       C  
+ATOM    149  CG  ASP A  20       0.620 -14.723 -41.766  1.00 64.33           C  
+ANISOU  149  CG  ASP A  20     8980   7254   8207    325   1414    288       C  
+ATOM    150  OD1 ASP A  20       1.122 -14.017 -42.690  1.00 70.08           O  
+ANISOU  150  OD1 ASP A  20     9639   8062   8926    341   1382    324       O  
+ATOM    151  OD2 ASP A  20       1.349 -15.271 -40.906  1.00 70.59           O  
+ANISOU  151  OD2 ASP A  20     9755   7971   9092    465   1489    432       O  
+ATOM    152  N   ASP A  21      -3.481 -14.806 -43.487  1.00 48.95           N  
+ANISOU  152  N   ASP A  21     7206   5550   5840   -269   1280   -332       N  
+ATOM    153  CA  ASP A  21      -4.886 -15.213 -43.792  1.00 52.07           C  
+ANISOU  153  CA  ASP A  21     7641   6029   6111   -489   1264   -547       C  
+ATOM    154  C   ASP A  21      -5.466 -16.364 -42.961  1.00 52.45           C  
+ANISOU  154  C   ASP A  21     7805   5898   6224   -586   1412   -652       C  
+ATOM    155  O   ASP A  21      -6.664 -16.621 -43.076  1.00 52.58           O  
+ANISOU  155  O   ASP A  21     7815   5996   6165   -785   1384   -823       O  
+ATOM    156  CB  ASP A  21      -5.080 -15.591 -45.251  1.00 52.20           C  
+ANISOU  156  CB  ASP A  21     7744   6142   5948   -620   1342   -716       C  
+ATOM    157  CG  ASP A  21      -4.192 -16.744 -45.675  1.00 54.79           C  
+ANISOU  157  CG  ASP A  21     8277   6240   6300   -591   1630   -772       C  
+ATOM    158  OD1 ASP A  21      -3.555 -17.399 -44.833  1.00 60.00           O  
+ANISOU  158  OD1 ASP A  21     9012   6660   7124   -475   1787   -678       O  
+ATOM    159  OD2 ASP A  21      -4.087 -16.978 -46.873  1.00 66.22           O  
+ANISOU  159  OD2 ASP A  21     9812   7754   7595   -664   1713   -895       O  
+ATOM    160  N   ASP A  22      -4.630 -17.059 -42.198  1.00 51.20           N  
+ANISOU  160  N   ASP A  22     7738   5513   6200   -447   1580   -538       N  
+ATOM    161  CA  ASP A  22      -5.098 -18.073 -41.256  1.00 62.00           C  
+ANISOU  161  CA  ASP A  22     9213   6691   7651   -492   1741   -573       C  
+ATOM    162  C   ASP A  22      -4.625 -17.744 -39.835  1.00 59.08           C  
+ANISOU  162  C   ASP A  22     8764   6294   7388   -296   1668   -346       C  
+ATOM    163  O   ASP A  22      -4.377 -18.629 -39.062  1.00 56.04           O  
+ANISOU  163  O   ASP A  22     8478   5724   7088   -214   1851   -264       O  
+ATOM    164  CB  ASP A  22      -4.624 -19.475 -41.714  1.00 71.33           C  
+ANISOU  164  CB  ASP A  22    10621   7602   8879   -509   2084   -652       C  
+ATOM    165  CG  ASP A  22      -3.093 -19.576 -41.838  1.00 78.00           C  
+ANISOU  165  CG  ASP A  22    11493   8340   9802   -254   2204   -448       C  
+ATOM    166  OD1 ASP A  22      -2.396 -18.536 -41.681  1.00 74.86           O  
+ANISOU  166  OD1 ASP A  22    10926   8102   9414   -102   2002   -272       O  
+ATOM    167  OD2 ASP A  22      -2.585 -20.697 -42.122  1.00 91.53           O  
+ANISOU  167  OD2 ASP A  22    13392   9804  11580   -212   2520   -469       O  
+ATOM    168  N   VAL A  23      -4.476 -16.441 -39.535  1.00 58.45           N  
+ANISOU  168  N   VAL A  23     8509   6406   7294   -222   1411   -246       N  
+ATOM    169  CA  VAL A  23      -4.282 -15.937 -38.191  1.00 51.17           C  
+ANISOU  169  CA  VAL A  23     7497   5521   6421    -98   1292    -96       C  
+ATOM    170  C   VAL A  23      -5.446 -15.027 -37.852  1.00 51.90           C  
+ANISOU  170  C   VAL A  23     7486   5767   6465   -205   1102   -177       C  
+ATOM    171  O   VAL A  23      -5.900 -14.243 -38.695  1.00 52.44           O  
+ANISOU  171  O   VAL A  23     7471   5973   6479   -287    979   -252       O  
+ATOM    172  CB  VAL A  23      -2.914 -15.295 -38.008  1.00 53.75           C  
+ANISOU  172  CB  VAL A  23     7721   5902   6798     84   1203     86       C  
+ATOM    173  CG1 VAL A  23      -2.782 -14.588 -36.643  1.00 51.64           C  
+ANISOU  173  CG1 VAL A  23     7345   5733   6542    168   1034    192       C  
+ATOM    174  CG2 VAL A  23      -1.872 -16.402 -38.166  1.00 52.89           C  
+ANISOU  174  CG2 VAL A  23     7712   5629   6754    219   1438    196       C  
+ATOM    175  N   TYR A  24      -6.020 -15.271 -36.669  1.00 49.92           N  
+ANISOU  175  N   TYR A  24     7252   5485   6229   -201   1118   -157       N  
+ATOM    176  CA  TYR A  24      -7.105 -14.448 -36.120  1.00 49.53           C  
+ANISOU  176  CA  TYR A  24     7107   5561   6149   -269    973   -210       C  
+ATOM    177  C   TYR A  24      -6.598 -13.062 -35.859  1.00 47.90           C  
+ANISOU  177  C   TYR A  24     6775   5477   5946   -174    771   -133       C  
+ATOM    178  O   TYR A  24      -5.530 -12.835 -35.330  1.00 50.41           O  
+ANISOU  178  O   TYR A  24     7074   5788   6289    -48    730    -19       O  
+ATOM    179  CB  TYR A  24      -7.664 -14.995 -34.792  1.00 53.15           C  
+ANISOU  179  CB  TYR A  24     7622   5953   6617   -252   1058   -177       C  
+ATOM    180  CG  TYR A  24      -8.368 -16.349 -34.905  1.00 54.34           C  
+ANISOU  180  CG  TYR A  24     7898   5950   6796   -378   1291   -263       C  
+ATOM    181  CD1 TYR A  24      -9.369 -16.572 -35.863  1.00 61.64           C  
+ANISOU  181  CD1 TYR A  24     8804   6911   7703   -595   1316   -450       C  
+ATOM    182  CD2 TYR A  24      -8.040 -17.385 -34.061  1.00 58.06           C  
+ANISOU  182  CD2 TYR A  24     8497   6251   7312   -288   1491   -157       C  
+ATOM    183  CE1 TYR A  24     -10.013 -17.808 -35.976  1.00 67.82           C  
+ANISOU  183  CE1 TYR A  24     9699   7540   8526   -757   1542   -565       C  
+ATOM    184  CE2 TYR A  24      -8.691 -18.634 -34.147  1.00 67.21           C  
+ANISOU  184  CE2 TYR A  24     9786   7220   8531   -418   1749   -239       C  
+ATOM    185  CZ  TYR A  24      -9.672 -18.847 -35.099  1.00 67.30           C  
+ANISOU  185  CZ  TYR A  24     9783   7246   8539   -670   1777   -462       C  
+ATOM    186  OH  TYR A  24     -10.304 -20.070 -35.167  1.00 63.80           O  
+ANISOU  186  OH  TYR A  24     9466   6605   8170   -838   2041   -574       O  
+ATOM    187  N   VAL A  25      -7.413 -12.132 -36.241  1.00 46.10           N  
+ANISOU  187  N   VAL A  25     6451   5365   5699   -242    655   -197       N  
+ATOM    188  CA  VAL A  25      -7.117 -10.720 -36.104  1.00 50.13           C  
+ANISOU  188  CA  VAL A  25     6853   5957   6237   -176    500   -147       C  
+ATOM    189  C   VAL A  25      -6.622 -10.284 -34.725  1.00 49.08           C  
+ANISOU  189  C   VAL A  25     6716   5810   6120    -88    441    -91       C  
+ATOM    190  O   VAL A  25      -5.602  -9.548 -34.601  1.00 48.80           O  
+ANISOU  190  O   VAL A  25     6626   5791   6124    -25    355    -35       O  
+ATOM    191  CB  VAL A  25      -8.407 -10.000 -36.511  1.00 51.95           C  
+ANISOU  191  CB  VAL A  25     6992   6297   6447   -248    438   -209       C  
+ATOM    192  CG1 VAL A  25      -8.482  -8.654 -35.889  1.00 65.37           C  
+ANISOU  192  CG1 VAL A  25     8616   8025   8196   -180    340   -173       C  
+ATOM    193  CG2 VAL A  25      -8.427  -9.935 -38.033  1.00 52.86           C  
+ANISOU  193  CG2 VAL A  25     7066   6496   6519   -296    427   -223       C  
+ATOM    194  N   LEU A  26      -7.301 -10.753 -33.681  1.00 50.45           N  
+ANISOU  194  N   LEU A  26     6944   5968   6256    -94    493   -112       N  
+ATOM    195  CA  LEU A  26      -6.902 -10.450 -32.290  1.00 47.33           C  
+ANISOU  195  CA  LEU A  26     6562   5597   5822    -14    443    -70       C  
+ATOM    196  C   LEU A  26      -5.498 -10.894 -32.035  1.00 47.06           C  
+ANISOU  196  C   LEU A  26     6537   5561   5781     82    436     39       C  
+ATOM    197  O   LEU A  26      -4.721 -10.194 -31.377  1.00 55.96           O  
+ANISOU  197  O   LEU A  26     7607   6768   6888    128    318     66       O  
+ATOM    198  CB  LEU A  26      -7.807 -11.200 -31.306  1.00 53.55           C  
+ANISOU  198  CB  LEU A  26     7430   6361   6552    -20    551    -79       C  
+ATOM    199  CG  LEU A  26      -7.510 -11.161 -29.801  1.00 55.13           C  
+ANISOU  199  CG  LEU A  26     7674   6613   6658     70    531    -26       C  
+ATOM    200  CD1 LEU A  26      -7.326  -9.720 -29.325  1.00 55.80           C  
+ANISOU  200  CD1 LEU A  26     7695   6785   6722     71    376    -95       C  
+ATOM    201  CD2 LEU A  26      -8.666 -11.852 -29.032  1.00 61.83           C  
+ANISOU  201  CD2 LEU A  26     8600   7428   7463     52    674    -33       C  
+ATOM    202  N   ASP A  27      -5.136 -12.069 -32.524  1.00 48.10           N  
+ANISOU  202  N   ASP A  27     6734   5609   5931    111    571    103       N  
+ATOM    203  CA  ASP A  27      -3.762 -12.587 -32.305  1.00 48.67           C  
+ANISOU  203  CA  ASP A  27     6797   5686   6010    241    594    251       C  
+ATOM    204  C   ASP A  27      -2.701 -11.814 -33.061  1.00 52.00           C  
+ANISOU  204  C   ASP A  27     7102   6157   6495    255    488    280       C  
+ATOM    205  O   ASP A  27      -1.619 -11.648 -32.546  1.00 53.84           O  
+ANISOU  205  O   ASP A  27     7252   6477   6725    342    414    382       O  
+ATOM    206  CB  ASP A  27      -3.670 -14.036 -32.649  1.00 52.61           C  
+ANISOU  206  CB  ASP A  27     7412   6040   6537    286    816    319       C  
+ATOM    207  CG  ASP A  27      -4.541 -14.887 -31.735  1.00 63.74           C  
+ANISOU  207  CG  ASP A  27     8934   7380   7902    289    954    332       C  
+ATOM    208  OD1 ASP A  27      -4.580 -14.630 -30.517  1.00 77.44           O  
+ANISOU  208  OD1 ASP A  27    10653   9216   9555    357    885    392       O  
+ATOM    209  OD2 ASP A  27      -5.228 -15.780 -32.232  1.00 66.17           O  
+ANISOU  209  OD2 ASP A  27     9347   7539   8253    206   1139    268       O  
+ATOM    210  N   ALA A  28      -3.001 -11.313 -34.254  1.00 45.81           N  
+ANISOU  210  N   ALA A  28     6297   5346   5763    172    479    200       N  
+ATOM    211  CA  ALA A  28      -2.052 -10.414 -34.921  1.00 45.27           C  
+ANISOU  211  CA  ALA A  28     6113   5321   5765    182    389    237       C  
+ATOM    212  C   ALA A  28      -1.874  -9.098 -34.113  1.00 46.76           C  
+ANISOU  212  C   ALA A  28     6200   5596   5968    152    219    201       C  
+ATOM    213  O   ALA A  28      -0.782  -8.604 -33.981  1.00 48.55           O  
+ANISOU  213  O   ALA A  28     6321   5880   6246    174    142    256       O  
+ATOM    214  CB  ALA A  28      -2.542 -10.096 -36.327  1.00 48.41           C  
+ANISOU  214  CB  ALA A  28     6517   5691   6185    111    423    175       C  
+ATOM    215  N   ALA A  29      -2.956  -8.547 -33.566  1.00 46.59           N  
+ANISOU  215  N   ALA A  29     6211   5582   5908     92    177     97       N  
+ATOM    216  CA  ALA A  29      -2.882  -7.367 -32.726  1.00 45.37           C  
+ANISOU  216  CA  ALA A  29     6001   5476   5760     54     58     28       C  
+ATOM    217  C   ALA A  29      -2.026  -7.590 -31.506  1.00 45.22           C  
+ANISOU  217  C   ALA A  29     5953   5566   5662     94    -18     63       C  
+ATOM    218  O   ALA A  29      -1.157  -6.760 -31.212  1.00 50.70           O  
+ANISOU  218  O   ALA A  29     6546   6327   6390     54   -129     39       O  
+ATOM    219  CB  ALA A  29      -4.268  -6.959 -32.299  1.00 45.68           C  
+ANISOU  219  CB  ALA A  29     6100   5492   5763     13     76    -74       C  
+ATOM    220  N   GLU A  30      -2.244  -8.704 -30.827  1.00 46.60           N  
+ANISOU  220  N   GLU A  30     6205   5769   5730    169     45    128       N  
+ATOM    221  CA  GLU A  30      -1.476  -9.042 -29.636  1.00 54.76           C  
+ANISOU  221  CA  GLU A  30     7206   6952   6646    243    -23    204       C  
+ATOM    222  C   GLU A  30      -0.050  -9.331 -29.955  1.00 54.21           C  
+ANISOU  222  C   GLU A  30     7010   6960   6626    313    -60    346       C  
+ATOM    223  O   GLU A  30       0.832  -8.823 -29.288  1.00 59.88           O  
+ANISOU  223  O   GLU A  30     7604   7849   7298    302   -205    354       O  
+ATOM    224  CB  GLU A  30      -2.122 -10.183 -28.852  1.00 62.74           C  
+ANISOU  224  CB  GLU A  30     8340   7960   7538    332     92    277       C  
+ATOM    225  CG  GLU A  30      -3.470  -9.711 -28.236  1.00 72.73           C  
+ANISOU  225  CG  GLU A  30     9697   9198   8739    260    106    134       C  
+ATOM    226  CD  GLU A  30      -4.256 -10.812 -27.471  1.00 84.77           C  
+ANISOU  226  CD  GLU A  30    11347  10699  10163    332    254    206       C  
+ATOM    227  OE1 GLU A  30      -4.358 -12.001 -27.950  1.00 80.99           O  
+ANISOU  227  OE1 GLU A  30    10932  10104   9737    384    419    311       O  
+ATOM    228  OE2 GLU A  30      -4.785 -10.463 -26.379  1.00 83.98           O  
+ANISOU  228  OE2 GLU A  30    11293  10681   9934    331    227    148       O  
+ATOM    229  N   GLU A  31       0.205 -10.073 -31.022  1.00 59.74           N  
+ANISOU  229  N   GLU A  31     7727   7548   7422    373     72    443       N  
+ATOM    230  CA  GLU A  31       1.574 -10.229 -31.535  1.00 56.65           C  
+ANISOU  230  CA  GLU A  31     7199   7210   7113    445     65    582       C  
+ATOM    231  C   GLU A  31       2.251  -8.862 -31.829  1.00 60.42           C  
+ANISOU  231  C   GLU A  31     7517   7754   7685    328    -85    505       C  
+ATOM    232  O   GLU A  31       3.462  -8.797 -31.776  1.00 66.23           O  
+ANISOU  232  O   GLU A  31     8087   8613   8463    365   -148    610       O  
+ATOM    233  CB  GLU A  31       1.536 -11.120 -32.771  1.00 64.23           C  
+ANISOU  233  CB  GLU A  31     8243   7999   8160    503    266    648       C  
+ATOM    234  CG  GLU A  31       2.861 -11.443 -33.471  1.00 83.36           C  
+ANISOU  234  CG  GLU A  31    10552  10436  10682    606    328    807       C  
+ATOM    235  CD  GLU A  31       3.790 -12.366 -32.669  1.00102.53           C  
+ANISOU  235  CD  GLU A  31    12908  12976  13073    795    367   1027       C  
+ATOM    236  OE1 GLU A  31       3.385 -12.888 -31.594  1.00113.60           O  
+ANISOU  236  OE1 GLU A  31    14374  14434  14355    859    366   1071       O  
+ATOM    237  OE2 GLU A  31       4.946 -12.569 -33.121  1.00102.50           O  
+ANISOU  237  OE2 GLU A  31    12770  13016  13158    898    412   1182       O  
+ATOM    238  N   ALA A  32       1.502  -7.778 -32.127  1.00 57.02           N  
+ANISOU  238  N   ALA A  32     7120   7240   7301    193   -126    339       N  
+ATOM    239  CA  ALA A  32       2.120  -6.424 -32.410  1.00 59.13           C  
+ANISOU  239  CA  ALA A  32     7255   7519   7692     72   -224    265       C  
+ATOM    240  C   ALA A  32       2.224  -5.516 -31.195  1.00 56.89           C  
+ANISOU  240  C   ALA A  32     6920   7349   7346    -41   -378    124       C  
+ATOM    241  O   ALA A  32       2.754  -4.418 -31.279  1.00 65.02           O  
+ANISOU  241  O   ALA A  32     7847   8373   8484   -167   -445     38       O  
+ATOM    242  CB  ALA A  32       1.377  -5.676 -33.506  1.00 53.40           C  
+ANISOU  242  CB  ALA A  32     6588   6626   7076     11   -149    198       C  
+ATOM    243  N   GLY A  33       1.719  -5.987 -30.077  1.00 55.56           N  
+ANISOU  243  N   GLY A  33     6832   7274   7000     -3   -414     93       N  
+ATOM    244  CA  GLY A  33       1.778  -5.257 -28.849  1.00 58.15           C  
+ANISOU  244  CA  GLY A  33     7139   7738   7215   -106   -550    -56       C  
+ATOM    245  C   GLY A  33       0.546  -4.451 -28.568  1.00 60.01           C  
+ANISOU  245  C   GLY A  33     7520   7837   7440   -190   -508   -246       C  
+ATOM    246  O   GLY A  33       0.620  -3.573 -27.741  1.00 69.82           O  
+ANISOU  246  O   GLY A  33     8758   9139   8629   -310   -593   -418       O  
+ATOM    247  N   ILE A  34      -0.586  -4.759 -29.224  1.00 61.19           N  
+ANISOU  247  N   ILE A  34     7792   7820   7635   -130   -370   -221       N  
+ATOM    248  CA  ILE A  34      -1.840  -4.017 -29.038  1.00 58.99           C  
+ANISOU  248  CA  ILE A  34     7627   7418   7368   -177   -306   -363       C  
+ATOM    249  C   ILE A  34      -2.765  -4.786 -28.094  1.00 62.15           C  
+ANISOU  249  C   ILE A  34     8149   7876   7589   -107   -261   -367       C  
+ATOM    250  O   ILE A  34      -3.056  -5.947 -28.343  1.00 63.50           O  
+ANISOU  250  O   ILE A  34     8359   8045   7721    -13   -186   -239       O  
+ATOM    251  CB  ILE A  34      -2.577  -3.788 -30.390  1.00 61.05           C  
+ANISOU  251  CB  ILE A  34     7905   7506   7785   -156   -191   -318       C  
+ATOM    252  CG1 ILE A  34      -1.701  -2.983 -31.385  1.00 65.68           C  
+ANISOU  252  CG1 ILE A  34     8381   8020   8552   -209   -201   -287       C  
+ATOM    253  CG2 ILE A  34      -3.890  -3.029 -30.184  1.00 63.01           C  
+ANISOU  253  CG2 ILE A  34     8237   7650   8053   -172   -114   -425       C  
+ATOM    254  CD1 ILE A  34      -2.244  -3.016 -32.822  1.00 63.49           C  
+ANISOU  254  CD1 ILE A  34     8108   7640   8375   -155    -98   -187       C  
+ATOM    255  N   ASP A  35      -3.244  -4.141 -27.030  1.00 63.70           N  
+ANISOU  255  N   ASP A  35     8416   8102   7682   -158   -279   -520       N  
+ATOM    256  CA  ASP A  35      -4.088  -4.826 -26.025  1.00 71.88           C  
+ANISOU  256  CA  ASP A  35     9569   9207   8534    -87   -222   -516       C  
+ATOM    257  C   ASP A  35      -5.567  -4.529 -26.307  1.00 64.56           C  
+ANISOU  257  C   ASP A  35     8725   8121   7682    -77    -78   -569       C  
+ATOM    258  O   ASP A  35      -6.130  -3.476 -25.980  1.00 66.69           O  
+ANISOU  258  O   ASP A  35     9040   8315   7983   -127    -40   -715       O  
+ATOM    259  CB  ASP A  35      -3.667  -4.503 -24.557  1.00 81.85           C  
+ANISOU  259  CB  ASP A  35    10862  10660   9575   -127   -325   -633       C  
+ATOM    260  CG  ASP A  35      -2.375  -5.278 -24.107  1.00 93.06           C  
+ANISOU  260  CG  ASP A  35    12178  12327  10851    -75   -463   -497       C  
+ATOM    261  OD1 ASP A  35      -2.081  -6.430 -24.567  1.00 87.57           O  
+ANISOU  261  OD1 ASP A  35    11448  11645  10179     50   -418   -279       O  
+ATOM    262  OD2 ASP A  35      -1.644  -4.712 -23.270  1.00100.07           O  
+ANISOU  262  OD2 ASP A  35    13013  13406  11600   -161   -608   -613       O  
+ATOM    263  N   LEU A  36      -6.157  -5.471 -27.010  1.00 61.66           N  
+ANISOU  263  N   LEU A  36     8363   7702   7362    -15     12   -444       N  
+ATOM    264  CA  LEU A  36      -7.533  -5.410 -27.353  1.00 56.54           C  
+ANISOU  264  CA  LEU A  36     7746   6959   6776     -6    133   -460       C  
+ATOM    265  C   LEU A  36      -8.274  -6.365 -26.418  1.00 58.83           C  
+ANISOU  265  C   LEU A  36     8125   7301   6925     45    227   -424       C  
+ATOM    266  O   LEU A  36      -7.725  -7.349 -25.938  1.00 59.91           O  
+ANISOU  266  O   LEU A  36     8295   7514   6951     96    222   -330       O  
+ATOM    267  CB  LEU A  36      -7.736  -5.829 -28.796  1.00 54.45           C  
+ANISOU  267  CB  LEU A  36     7414   6631   6642     -9    169   -370       C  
+ATOM    268  CG  LEU A  36      -7.150  -4.979 -29.924  1.00 47.43           C  
+ANISOU  268  CG  LEU A  36     6437   5685   5896    -39    115   -362       C  
+ATOM    269  CD1 LEU A  36      -7.661  -5.559 -31.235  1.00 51.84           C  
+ANISOU  269  CD1 LEU A  36     6953   6228   6515    -36    168   -282       C  
+ATOM    270  CD2 LEU A  36      -7.550  -3.538 -29.754  1.00 48.45           C  
+ANISOU  270  CD2 LEU A  36     6559   5739   6109    -60    130   -458       C  
+ATOM    271  N   PRO A  37      -9.531  -6.066 -26.158  1.00 52.73           N  
+ANISOU  271  N   PRO A  37     7383   6483   6166     48    333   -477       N  
+ATOM    272  CA  PRO A  37     -10.189  -6.803 -25.130  1.00 48.70           C  
+ANISOU  272  CA  PRO A  37     6960   6021   5521     94    437   -451       C  
+ATOM    273  C   PRO A  37     -10.579  -8.210 -25.630  1.00 53.45           C  
+ANISOU  273  C   PRO A  37     7558   6591   6158    100    538   -324       C  
+ATOM    274  O   PRO A  37     -10.785  -8.477 -26.837  1.00 49.32           O  
+ANISOU  274  O   PRO A  37     6961   6008   5767     49    548   -299       O  
+ATOM    275  CB  PRO A  37     -11.382  -5.907 -24.791  1.00 51.49           C  
+ANISOU  275  CB  PRO A  37     7326   6326   5910     95    535   -549       C  
+ATOM    276  CG  PRO A  37     -11.712  -5.243 -26.095  1.00 57.15           C  
+ANISOU  276  CG  PRO A  37     7927   6960   6825     64    521   -547       C  
+ATOM    277  CD  PRO A  37     -10.372  -5.018 -26.760  1.00 53.71           C  
+ANISOU  277  CD  PRO A  37     7454   6520   6432     30    379   -538       C  
+ATOM    278  N   TYR A  38     -10.593  -9.140 -24.698  1.00 52.25           N  
+ANISOU  278  N   TYR A  38     7494   6481   5875    159    621   -244       N  
+ATOM    279  CA  TYR A  38     -11.096 -10.464 -24.975  1.00 58.41           C  
+ANISOU  279  CA  TYR A  38     8299   7189   6702    152    774   -141       C  
+ATOM    280  C   TYR A  38     -11.545 -11.071 -23.664  1.00 53.69           C  
+ANISOU  280  C   TYR A  38     7809   6629   5962    227    913    -70       C  
+ATOM    281  O   TYR A  38     -11.164 -10.607 -22.581  1.00 52.44           O  
+ANISOU  281  O   TYR A  38     7709   6589   5625    301    856    -82       O  
+ATOM    282  CB  TYR A  38      -9.996 -11.359 -25.594  1.00 54.60           C  
+ANISOU  282  CB  TYR A  38     7821   6673   6252    178    755    -32       C  
+ATOM    283  CG  TYR A  38      -8.783 -11.536 -24.706  1.00 57.28           C  
+ANISOU  283  CG  TYR A  38     8199   7128   6435    299    678     70       C  
+ATOM    284  CD1 TYR A  38      -7.743 -10.603 -24.717  1.00 57.17           C  
+ANISOU  284  CD1 TYR A  38     8115   7222   6383    300    480     19       C  
+ATOM    285  CD2 TYR A  38      -8.679 -12.620 -23.830  1.00 58.87           C  
+ANISOU  285  CD2 TYR A  38     8492   7349   6525    412    809    232       C  
+ATOM    286  CE1 TYR A  38      -6.629 -10.752 -23.885  1.00 58.64           C  
+ANISOU  286  CE1 TYR A  38     8295   7574   6409    396    383    113       C  
+ATOM    287  CE2 TYR A  38      -7.565 -12.768 -22.985  1.00 62.26           C  
+ANISOU  287  CE2 TYR A  38     8928   7946   6781    545    722    358       C  
+ATOM    288  CZ  TYR A  38      -6.548 -11.837 -23.032  1.00 65.34           C  
+ANISOU  288  CZ  TYR A  38     9221   8482   7122    529    494    291       C  
+ATOM    289  OH  TYR A  38      -5.464 -11.963 -22.208  1.00 72.76           O  
+ANISOU  289  OH  TYR A  38    10126   9640   7877    642    383    410       O  
+ATOM    290  N   SER A  39     -12.264 -12.176 -23.765  1.00 51.04           N  
+ANISOU  290  N   SER A  39     7503   6198   5691    202   1102      6       N  
+ATOM    291  CA  SER A  39     -12.527 -12.977 -22.556  1.00 52.70           C  
+ANISOU  291  CA  SER A  39     7828   6422   5770    296   1272    129       C  
+ATOM    292  C   SER A  39     -12.586 -14.475 -22.933  1.00 54.61           C  
+ANISOU  292  C   SER A  39     8121   6509   6118    281   1473    260       C  
+ATOM    293  O   SER A  39     -11.697 -15.196 -22.537  1.00 53.05           O  
+ANISOU  293  O   SER A  39     8000   6314   5842    404   1512    419       O  
+ATOM    294  CB  SER A  39     -13.752 -12.480 -21.786  1.00 50.63           C  
+ANISOU  294  CB  SER A  39     7578   6193   5466    287   1376     64       C  
+ATOM    295  OG  SER A  39     -14.134 -13.447 -20.804  1.00 57.92           O  
+ANISOU  295  OG  SER A  39     8608   7099   6297    364   1590    207       O  
+ATOM    296  N   CYS A  40     -13.549 -14.932 -23.748  1.00 56.78           N  
+ANISOU  296  N   CYS A  40     8345   6653   6573    127   1599    192       N  
+ATOM    297  CA  CYS A  40     -13.634 -16.380 -24.053  1.00 57.29           C  
+ANISOU  297  CA  CYS A  40     8484   6532   6749     80   1830    281       C  
+ATOM    298  C   CYS A  40     -12.645 -16.882 -25.075  1.00 62.77           C  
+ANISOU  298  C   CYS A  40     9192   7133   7523     67   1795    293       C  
+ATOM    299  O   CYS A  40     -12.278 -18.037 -25.022  1.00 51.88           O  
+ANISOU  299  O   CYS A  40     7920   5599   6191    114   1993    416       O  
+ATOM    300  CB  CYS A  40     -15.040 -16.831 -24.469  1.00 62.61           C  
+ANISOU  300  CB  CYS A  40     9100   7107   7580   -117   2004    185       C  
+ATOM    301  SG  CYS A  40     -15.521 -16.463 -26.163  1.00 58.56           S  
+ANISOU  301  SG  CYS A  40     8420   6610   7220   -350   1871    -25       S  
+ATOM    302  N   ARG A  41     -12.233 -16.028 -26.016  1.00 58.00           N  
+ANISOU  302  N   ARG A  41     8486   6605   6943     14   1575    175       N  
+ATOM    303  CA  ARG A  41     -11.317 -16.429 -27.087  1.00 58.21           C  
+ANISOU  303  CA  ARG A  41     8521   6552   7044     -1   1548    175       C  
+ATOM    304  C   ARG A  41     -11.821 -17.585 -27.916  1.00 57.79           C  
+ANISOU  304  C   ARG A  41     8520   6302   7133   -157   1766    115       C  
+ATOM    305  O   ARG A  41     -10.986 -18.264 -28.554  1.00 62.26           O  
+ANISOU  305  O   ARG A  41     9155   6747   7753   -132   1841    152       O  
+ATOM    306  CB  ARG A  41      -9.896 -16.763 -26.569  1.00 63.76           C  
+ANISOU  306  CB  ARG A  41     9289   7271   7664    206   1533    363       C  
+ATOM    307  CG  ARG A  41      -9.186 -15.605 -25.856  1.00 71.18           C  
+ANISOU  307  CG  ARG A  41    10160   8433   8450    322   1286    387       C  
+ATOM    308  CD  ARG A  41      -7.710 -15.932 -25.568  1.00 80.04           C  
+ANISOU  308  CD  ARG A  41    11287   9622   9501    504   1238    570       C  
+ATOM    309  NE  ARG A  41      -6.866 -15.741 -26.762  1.00 74.82           N  
+ANISOU  309  NE  ARG A  41    10554   8929   8944    472   1145    532       N  
+ATOM    310  CZ  ARG A  41      -6.356 -14.582 -27.159  1.00 78.00           C  
+ANISOU  310  CZ  ARG A  41    10841   9455   9338    432    915    438       C  
+ATOM    311  NH1 ARG A  41      -6.552 -13.467 -26.465  1.00 81.90           N  
+ANISOU  311  NH1 ARG A  41    11285  10102   9732    410    749    350       N  
+ATOM    312  NH2 ARG A  41      -5.644 -14.532 -28.265  1.00 86.15           N  
+ANISOU  312  NH2 ARG A  41    11819  10442  10471    411    877    426       N  
+ATOM    313  N   ALA A  42     -13.150 -17.769 -27.971  1.00 49.81           N  
+ANISOU  313  N   ALA A  42     7468   5266   6189   -330   1868      7       N  
+ATOM    314  CA  ALA A  42     -13.768 -18.969 -28.558  1.00 57.96           C  
+ANISOU  314  CA  ALA A  42     8557   6104   7358   -524   2112    -75       C  
+ATOM    315  C   ALA A  42     -14.982 -18.639 -29.396  1.00 57.37           C  
+ANISOU  315  C   ALA A  42     8326   6129   7343   -777   2047   -282       C  
+ATOM    316  O   ALA A  42     -15.740 -19.526 -29.769  1.00 64.20           O  
+ANISOU  316  O   ALA A  42     9200   6877   8312   -990   2234   -389       O  
+ATOM    317  CB  ALA A  42     -14.200 -19.960 -27.458  1.00 56.47           C  
+ANISOU  317  CB  ALA A  42     8492   5754   7210   -482   2407     58       C  
+ATOM    318  N   GLY A  43     -15.231 -17.380 -29.635  1.00 52.54           N  
+ANISOU  318  N   GLY A  43     7557   5735   6668   -759   1799   -332       N  
+ATOM    319  CA  GLY A  43     -16.309 -17.040 -30.539  1.00 57.00           C  
+ANISOU  319  CA  GLY A  43     7941   6441   7273   -969   1718   -492       C  
+ATOM    320  C   GLY A  43     -17.684 -17.010 -29.934  1.00 58.47           C  
+ANISOU  320  C   GLY A  43     8011   6695   7510  -1063   1807   -511       C  
+ATOM    321  O   GLY A  43     -18.693 -16.858 -30.667  1.00 64.87           O  
+ANISOU  321  O   GLY A  43     8633   7651   8361  -1255   1754   -633       O  
+ATOM    322  N   SER A  44     -17.753 -17.088 -28.605  1.00 57.15           N  
+ANISOU  322  N   SER A  44     7930   6459   7323   -922   1931   -379       N  
+ATOM    323  CA  SER A  44     -19.057 -17.205 -27.927  1.00 59.58           C  
+ANISOU  323  CA  SER A  44     8144   6800   7692  -1003   2076   -376       C  
+ATOM    324  C   SER A  44     -19.354 -16.159 -26.851  1.00 51.98           C  
+ANISOU  324  C   SER A  44     7145   5959   6646   -810   2021   -281       C  
+ATOM    325  O   SER A  44     -20.144 -16.385 -25.952  1.00 58.60           O  
+ANISOU  325  O   SER A  44     7978   6778   7507   -803   2197   -224       O  
+ATOM    326  CB  SER A  44     -19.181 -18.630 -27.398  1.00 63.12           C  
+ANISOU  326  CB  SER A  44     8744   7008   8228  -1080   2393   -327       C  
+ATOM    327  OG  SER A  44     -17.989 -18.942 -26.691  1.00 75.47           O  
+ANISOU  327  OG  SER A  44    10522   8441   9708   -852   2451   -164       O  
+ATOM    328  N   CYS A  45     -18.785 -14.973 -26.981  1.00 51.65           N  
+ANISOU  328  N   CYS A  45     7072   6035   6515   -668   1796   -279       N  
+ATOM    329  CA  CYS A  45     -19.057 -13.886 -26.059  1.00 48.70           C  
+ANISOU  329  CA  CYS A  45     6677   5758   6066   -505   1753   -233       C  
+ATOM    330  C   CYS A  45     -18.893 -12.526 -26.780  1.00 51.12           C  
+ANISOU  330  C   CYS A  45     6860   6197   6366   -453   1521   -288       C  
+ATOM    331  O   CYS A  45     -18.542 -12.469 -27.980  1.00 50.80           O  
+ANISOU  331  O   CYS A  45     6749   6191   6360   -532   1388   -341       O  
+ATOM    332  CB  CYS A  45     -18.171 -13.989 -24.805  1.00 50.90           C  
+ANISOU  332  CB  CYS A  45     7166   5974   6198   -316   1803   -126       C  
+ATOM    333  SG  CYS A  45     -16.566 -13.180 -24.911  1.00 53.21           S  
+ANISOU  333  SG  CYS A  45     7542   6307   6366   -170   1556   -124       S  
+ATOM    334  N   SER A  46     -19.167 -11.439 -26.041  1.00 49.49           N  
+ANISOU  334  N   SER A  46     6640   6051   6114   -315   1503   -272       N  
+ATOM    335  CA  SER A  46     -19.261 -10.117 -26.614  1.00 49.31           C  
+ANISOU  335  CA  SER A  46     6494   6118   6122   -255   1356   -304       C  
+ATOM    336  C   SER A  46     -17.941  -9.369 -26.532  1.00 51.44           C  
+ANISOU  336  C   SER A  46     6888   6345   6311   -146   1208   -320       C  
+ATOM    337  O   SER A  46     -17.854  -8.268 -27.057  1.00 46.10           O  
+ANISOU  337  O   SER A  46     6135   5703   5678    -96   1103   -340       O  
+ATOM    338  CB  SER A  46     -20.298  -9.307 -25.871  1.00 50.14           C  
+ANISOU  338  CB  SER A  46     6525   6274   6249   -163   1462   -287       C  
+ATOM    339  OG  SER A  46     -19.973  -9.287 -24.483  1.00 49.91           O  
+ANISOU  339  OG  SER A  46     6691   6179   6094    -53   1563   -278       O  
+ATOM    340  N   SER A  47     -16.939  -9.950 -25.880  1.00 47.00           N  
+ANISOU  340  N   SER A  47     6498   5716   5641   -106   1210   -297       N  
+ATOM    341  CA  SER A  47     -15.839  -9.148 -25.341  1.00 48.40           C  
+ANISOU  341  CA  SER A  47     6782   5891   5713     -1   1093   -321       C  
+ATOM    342  C   SER A  47     -14.884  -8.548 -26.378  1.00 50.48           C  
+ANISOU  342  C   SER A  47     6998   6152   6030    -15    913   -348       C  
+ATOM    343  O   SER A  47     -14.433  -7.391 -26.220  1.00 42.86           O  
+ANISOU  343  O   SER A  47     6043   5186   5055     37    827   -403       O  
+ATOM    344  CB  SER A  47     -15.052  -9.964 -24.335  1.00 48.69           C  
+ANISOU  344  CB  SER A  47     6981   5919   5599     58   1134   -259       C  
+ATOM    345  OG  SER A  47     -14.042  -9.148 -23.822  1.00 52.57           O  
+ANISOU  345  OG  SER A  47     7538   6457   5976    130    999   -303       O  
+ATOM    346  N   CYS A  48     -14.586  -9.312 -27.432  1.00 46.30           N  
+ANISOU  346  N   CYS A  48     6426   5606   5560    -94    881   -320       N  
+ATOM    347  CA  CYS A  48     -13.615  -8.899 -28.445  1.00 43.55           C  
+ANISOU  347  CA  CYS A  48     6042   5255   5251   -102    736   -325       C  
+ATOM    348  C   CYS A  48     -14.282  -8.264 -29.667  1.00 48.19           C  
+ANISOU  348  C   CYS A  48     6472   5897   5938   -148    687   -339       C  
+ATOM    349  O   CYS A  48     -13.664  -8.163 -30.727  1.00 52.68           O  
+ANISOU  349  O   CYS A  48     7001   6475   6538   -171    598   -328       O  
+ATOM    350  CB  CYS A  48     -12.855 -10.140 -28.938  1.00 45.20           C  
+ANISOU  350  CB  CYS A  48     6309   5413   5450   -145    755   -280       C  
+ATOM    351  SG  CYS A  48     -13.936 -11.252 -29.869  1.00 49.74           S  
+ANISOU  351  SG  CYS A  48     6821   5979   6098   -304    875   -312       S  
+ATOM    352  N   ALA A  49     -15.536  -7.842 -29.543  1.00 49.80           N  
+ANISOU  352  N   ALA A  49     6575   6158   6186   -145    751   -344       N  
+ATOM    353  CA  ALA A  49     -16.294  -7.449 -30.708  1.00 48.00           C  
+ANISOU  353  CA  ALA A  49     6167   6039   6032   -181    710   -321       C  
+ATOM    354  C   ALA A  49     -15.698  -6.209 -31.365  1.00 47.62           C  
+ANISOU  354  C   ALA A  49     6079   5983   6030    -94    608   -287       C  
+ATOM    355  O   ALA A  49     -15.183  -5.313 -30.693  1.00 45.45           O  
+ANISOU  355  O   ALA A  49     5885   5614   5769     -6    608   -304       O  
+ATOM    356  CB  ALA A  49     -17.720  -7.170 -30.327  1.00 44.89           C  
+ANISOU  356  CB  ALA A  49     5646   5725   5684   -164    808   -302       C  
+ATOM    357  N   GLY A  50     -15.818  -6.151 -32.678  1.00 48.69           N  
+ANISOU  357  N   GLY A  50     6091   6224   6184   -128    536   -244       N  
+ATOM    358  CA  GLY A  50     -15.449  -4.952 -33.442  1.00 49.68           C  
+ANISOU  358  CA  GLY A  50     6154   6355   6367    -31    471   -170       C  
+ATOM    359  C   GLY A  50     -16.413  -4.732 -34.592  1.00 50.54           C  
+ANISOU  359  C   GLY A  50     6054   6667   6481    -27    438    -81       C  
+ATOM    360  O   GLY A  50     -17.402  -5.446 -34.760  1.00 51.08           O  
+ANISOU  360  O   GLY A  50     6008   6888   6512   -119    451    -99       O  
+ATOM    361  N   LYS A  51     -16.125  -3.748 -35.412  1.00 53.55           N  
+ANISOU  361  N   LYS A  51     6371   7070   6904     74    397     23       N  
+ATOM    362  CA  LYS A  51     -16.949  -3.502 -36.568  1.00 53.87           C  
+ANISOU  362  CA  LYS A  51     6201   7352   6915    104    349    142       C  
+ATOM    363  C   LYS A  51     -16.099  -3.324 -37.812  1.00 52.01           C  
+ANISOU  363  C   LYS A  51     5967   7166   6626    116    266    208       C  
+ATOM    364  O   LYS A  51     -15.259  -2.429 -37.884  1.00 49.83           O  
+ANISOU  364  O   LYS A  51     5763   6736   6431    222    288    275       O  
+ATOM    365  CB  LYS A  51     -17.819  -2.272 -36.354  1.00 55.11           C  
+ANISOU  365  CB  LYS A  51     6228   7529   7182    289    432    285       C  
+ATOM    366  CG  LYS A  51     -19.060  -2.302 -37.241  1.00 69.25           C  
+ANISOU  366  CG  LYS A  51     7743   9649   8918    311    386    414       C  
+ATOM    367  CD  LYS A  51     -19.994  -1.116 -37.036  1.00 78.14           C  
+ANISOU  367  CD  LYS A  51     8713  10807  10169    534    496    599       C  
+ATOM    368  CE  LYS A  51     -19.697  -0.098 -38.130  1.00 91.14           C  
+ANISOU  368  CE  LYS A  51    10279  12512  11835    709    478    813       C  
+ATOM    369  NZ  LYS A  51     -20.322   1.238 -37.924  1.00 98.12           N  
+ANISOU  369  NZ  LYS A  51    11067  13328  12884    974    639   1022       N  
+ATOM    370  N   VAL A  52     -16.371  -4.149 -38.805  1.00 56.50           N  
+ANISOU  370  N   VAL A  52     6451   7958   7057     -1    184    184       N  
+ATOM    371  CA  VAL A  52     -15.743  -4.044 -40.096  1.00 53.02           C  
+ANISOU  371  CA  VAL A  52     5995   7623   6524     10    113    251       C  
+ATOM    372  C   VAL A  52     -16.271  -2.823 -40.812  1.00 55.66           C  
+ANISOU  372  C   VAL A  52     6153   8116   6878    198    104    478       C  
+ATOM    373  O   VAL A  52     -17.446  -2.763 -41.107  1.00 57.54           O  
+ANISOU  373  O   VAL A  52     6184   8614   7061    218     71    553       O  
+ATOM    374  CB  VAL A  52     -16.050  -5.263 -40.957  1.00 52.46           C  
+ANISOU  374  CB  VAL A  52     5882   7779   6271   -184     41    135       C  
+ATOM    375  CG1 VAL A  52     -15.519  -5.033 -42.382  1.00 54.82           C  
+ANISOU  375  CG1 VAL A  52     6153   8239   6436   -149    -26    221       C  
+ATOM    376  CG2 VAL A  52     -15.383  -6.462 -40.332  1.00 50.36           C  
+ANISOU  376  CG2 VAL A  52     5817   7306   6010   -339     95    -55       C  
+ATOM    377  N   VAL A  53     -15.394  -1.848 -41.054  1.00 54.66           N  
+ANISOU  377  N   VAL A  53     6097   7828   6843    341    150    599       N  
+ATOM    378  CA  VAL A  53     -15.763  -0.629 -41.772  1.00 62.36           C  
+ANISOU  378  CA  VAL A  53     6930   8905   7859    554    184    855       C  
+ATOM    379  C   VAL A  53     -15.275  -0.645 -43.240  1.00 58.73           C  
+ANISOU  379  C   VAL A  53     6429   8643   7241    577    116    972       C  
+ATOM    380  O   VAL A  53     -15.785   0.085 -44.048  1.00 58.59           O  
+ANISOU  380  O   VAL A  53     6253   8828   7179    741    116   1203       O  
+ATOM    381  CB  VAL A  53     -15.351   0.680 -41.005  1.00 65.49           C  
+ANISOU  381  CB  VAL A  53     7415   8968   8500    719    338    940       C  
+ATOM    382  CG1 VAL A  53     -15.576   0.504 -39.522  1.00 72.86           C  
+ANISOU  382  CG1 VAL A  53     8446   9701   9533    655    398    764       C  
+ATOM    383  CG2 VAL A  53     -13.917   1.090 -41.248  1.00 68.64           C  
+ANISOU  383  CG2 VAL A  53     7968   9134   8977    721    376    943       C  
+ATOM    384  N   SER A  54     -14.348  -1.525 -43.591  1.00 53.74           N  
+ANISOU  384  N   SER A  54     5935   7975   6509    426     68    825       N  
+ATOM    385  CA  SER A  54     -13.884  -1.675 -44.972  1.00 55.87           C  
+ANISOU  385  CA  SER A  54     6190   8441   6597    431     18    904       C  
+ATOM    386  C   SER A  54     -13.173  -3.046 -45.081  1.00 56.25           C  
+ANISOU  386  C   SER A  54     6394   8450   6527    213    -15    660       C  
+ATOM    387  O   SER A  54     -12.486  -3.512 -44.129  1.00 49.66           O  
+ANISOU  387  O   SER A  54     5714   7335   5817    133     33    511       O  
+ATOM    388  CB  SER A  54     -12.991  -0.455 -45.367  1.00 56.61           C  
+ANISOU  388  CB  SER A  54     6326   8357   6824    625    121   1123       C  
+ATOM    389  OG  SER A  54     -12.138  -0.710 -46.445  1.00 63.73           O  
+ANISOU  389  OG  SER A  54     7288   9336   7589    611    112   1159       O  
+ATOM    390  N   GLY A  55     -13.389  -3.710 -46.217  1.00 53.71           N  
+ANISOU  390  N   GLY A  55     6028   8423   5956    121    -89    620       N  
+ATOM    391  CA  GLY A  55     -12.890  -5.055 -46.464  1.00 54.03           C  
+ANISOU  391  CA  GLY A  55     6214   8444   5869    -87    -89    381       C  
+ATOM    392  C   GLY A  55     -13.780  -6.179 -45.936  1.00 56.10           C  
+ANISOU  392  C   GLY A  55     6459   8774   6082   -306   -121    151       C  
+ATOM    393  O   GLY A  55     -14.982  -5.983 -45.681  1.00 60.55           O  
+ANISOU  393  O   GLY A  55     6840   9527   6637   -318   -183    180       O  
+ATOM    394  N   SER A  56     -13.181  -7.362 -45.781  1.00 52.30           N  
+ANISOU  394  N   SER A  56     6161   8128   5583   -472    -54    -60       N  
+ATOM    395  CA  SER A  56     -13.909  -8.555 -45.414  1.00 56.19           C  
+ANISOU  395  CA  SER A  56     6669   8647   6032   -704    -41   -291       C  
+ATOM    396  C   SER A  56     -13.104  -9.443 -44.480  1.00 53.82           C  
+ANISOU  396  C   SER A  56     6589   7981   5876   -764     94   -420       C  
+ATOM    397  O   SER A  56     -11.877  -9.347 -44.370  1.00 54.78           O  
+ANISOU  397  O   SER A  56     6852   7882   6078   -658    162   -364       O  
+ATOM    398  CB  SER A  56     -14.330  -9.330 -46.692  1.00 60.27           C  
+ANISOU  398  CB  SER A  56     7153   9473   6272   -904    -92   -449       C  
+ATOM    399  OG  SER A  56     -13.185  -9.640 -47.492  1.00 64.49           O  
+ANISOU  399  OG  SER A  56     7867   9923   6713   -890    -21   -484       O  
+ATOM    400  N   VAL A  57     -13.818 -10.317 -43.788  1.00 57.62           N  
+ANISOU  400  N   VAL A  57     7081   8413   6396   -929    142   -574       N  
+ATOM    401  CA  VAL A  57     -13.221 -11.309 -42.892  1.00 53.60           C  
+ANISOU  401  CA  VAL A  57     6773   7581   6008   -986    293   -680       C  
+ATOM    402  C   VAL A  57     -13.972 -12.587 -43.112  1.00 55.21           C  
+ANISOU  402  C   VAL A  57     7008   7830   6138  -1256    368   -912       C  
+ATOM    403  O   VAL A  57     -15.069 -12.588 -43.684  1.00 53.95           O  
+ANISOU  403  O   VAL A  57     6676   7964   5858  -1404    275   -989       O  
+ATOM    404  CB  VAL A  57     -13.373 -10.956 -41.381  1.00 57.18           C  
+ANISOU  404  CB  VAL A  57     7224   7857   6644   -880    320   -596       C  
+ATOM    405  CG1 VAL A  57     -12.463  -9.803 -41.015  1.00 52.19           C  
+ANISOU  405  CG1 VAL A  57     6602   7118   6107   -653    277   -417       C  
+ATOM    406  CG2 VAL A  57     -14.834 -10.627 -41.047  1.00 53.61           C  
+ANISOU  406  CG2 VAL A  57     6573   7599   6197   -936    258   -594       C  
+ATOM    407  N   ASP A  58     -13.366 -13.666 -42.641  1.00 55.82           N  
+ANISOU  407  N   ASP A  58     7294   7617   6296  -1318    547  -1013       N  
+ATOM    408  CA  ASP A  58     -13.996 -14.957 -42.561  1.00 58.46           C  
+ANISOU  408  CA  ASP A  58     7701   7878   6631  -1574    687  -1233       C  
+ATOM    409  C   ASP A  58     -14.136 -15.223 -41.085  1.00 55.65           C  
+ANISOU  409  C   ASP A  58     7395   7287   6461  -1515    794  -1166       C  
+ATOM    410  O   ASP A  58     -13.156 -15.457 -40.418  1.00 55.05           O  
+ANISOU  410  O   ASP A  58     7478   6953   6484  -1367    903  -1074       O  
+ATOM    411  CB  ASP A  58     -13.103 -16.016 -43.188  1.00 65.76           C  
+ANISOU  411  CB  ASP A  58     8862   8605   7518  -1656    869  -1374       C  
+ATOM    412  CG  ASP A  58     -13.609 -17.451 -42.970  1.00 72.39           C  
+ANISOU  412  CG  ASP A  58     9833   9259   8413  -1919   1088  -1606       C  
+ATOM    413  OD1 ASP A  58     -14.654 -17.719 -42.304  1.00 72.82           O  
+ANISOU  413  OD1 ASP A  58     9792   9332   8542  -2058   1107  -1663       O  
+ATOM    414  OD2 ASP A  58     -12.932 -18.339 -43.523  1.00 80.41           O  
+ANISOU  414  OD2 ASP A  58    11056  10090   9406  -1990   1274  -1737       O  
+ATOM    415  N   GLN A  59     -15.358 -15.182 -40.586  1.00 59.22           N  
+ANISOU  415  N   GLN A  59     7695   7858   6947  -1623    763  -1198       N  
+ATOM    416  CA  GLN A  59     -15.612 -15.422 -39.174  1.00 62.73           C  
+ANISOU  416  CA  GLN A  59     8181   8107   7544  -1569    878  -1130       C  
+ATOM    417  C   GLN A  59     -16.694 -16.457 -38.993  1.00 65.10           C  
+ANISOU  417  C   GLN A  59     8454   8390   7889  -1842   1015  -1303       C  
+ATOM    418  O   GLN A  59     -17.576 -16.295 -38.154  1.00 66.15           O  
+ANISOU  418  O   GLN A  59     8471   8562   8101  -1853   1028  -1256       O  
+ATOM    419  CB  GLN A  59     -16.011 -14.137 -38.463  1.00 57.25           C  
+ANISOU  419  CB  GLN A  59     7325   7538   6889  -1378    738   -953       C  
+ATOM    420  CG  GLN A  59     -17.246 -13.434 -39.016  1.00 55.97           C  
+ANISOU  420  CG  GLN A  59     6886   7717   6661  -1449    585   -955       C  
+ATOM    421  CD  GLN A  59     -17.652 -12.296 -38.096  1.00 62.04           C  
+ANISOU  421  CD  GLN A  59     7537   8522   7511  -1245    528   -780       C  
+ATOM    422  OE1 GLN A  59     -18.210 -11.269 -38.534  1.00 66.81           O  
+ANISOU  422  OE1 GLN A  59     7938   9366   8079  -1159    394   -682       O  
+ATOM    423  NE2 GLN A  59     -17.359 -12.461 -36.800  1.00 56.51           N  
+ANISOU  423  NE2 GLN A  59     6972   7583   6913  -1150    646   -731       N  
+ATOM    424  N   SER A  60     -16.585 -17.512 -39.786  1.00 64.01           N  
+ANISOU  424  N   SER A  60     8432   8180   7707  -2067   1137  -1510       N  
+ATOM    425  CA  SER A  60     -17.358 -18.738 -39.660  1.00 71.88           C  
+ANISOU  425  CA  SER A  60     9472   9060   8776  -2367   1339  -1715       C  
+ATOM    426  C   SER A  60     -17.042 -19.592 -38.399  1.00 69.57           C  
+ANISOU  426  C   SER A  60     9386   8371   8673  -2297   1620  -1638       C  
+ATOM    427  O   SER A  60     -17.817 -20.492 -38.073  1.00 71.72           O  
+ANISOU  427  O   SER A  60     9674   8528   9048  -2526   1809  -1764       O  
+ATOM    428  CB  SER A  60     -17.104 -19.609 -40.916  1.00 74.82           C  
+ANISOU  428  CB  SER A  60     9970   9417   9042  -2615   1424  -1979       C  
+ATOM    429  OG  SER A  60     -15.720 -19.921 -40.981  1.00 69.57           O  
+ANISOU  429  OG  SER A  60     9563   8467   8400  -2430   1560  -1910       O  
+ATOM    430  N   ASP A  61     -15.919 -19.358 -37.720  1.00 66.51           N  
+ANISOU  430  N   ASP A  61     9149   7790   8330  -1996   1657  -1429       N  
+ATOM    431  CA  ASP A  61     -15.690 -19.995 -36.412  1.00 71.53           C  
+ANISOU  431  CA  ASP A  61     9937   8131   9109  -1878   1886  -1294       C  
+ATOM    432  C   ASP A  61     -16.401 -19.243 -35.270  1.00 70.72           C  
+ANISOU  432  C   ASP A  61     9687   8145   9037  -1762   1797  -1144       C  
+ATOM    433  O   ASP A  61     -16.415 -19.738 -34.176  1.00 76.22           O  
+ANISOU  433  O   ASP A  61    10486   8652   9822  -1683   1980  -1036       O  
+ATOM    434  CB  ASP A  61     -14.215 -20.094 -36.049  1.00 71.97           C  
+ANISOU  434  CB  ASP A  61    10185   7978   9182  -1596   1957  -1113       C  
+ATOM    435  CG  ASP A  61     -13.386 -20.780 -37.089  1.00 73.12           C  
+ANISOU  435  CG  ASP A  61    10490   7983   9309  -1651   2076  -1223       C  
+ATOM    436  OD1 ASP A  61     -13.929 -21.468 -37.992  1.00 83.53           O  
+ANISOU  436  OD1 ASP A  61    11838   9288  10611  -1938   2174  -1474       O  
+ATOM    437  OD2 ASP A  61     -12.154 -20.643 -36.976  1.00 81.02           O  
+ANISOU  437  OD2 ASP A  61    11586   8889  10308  -1407   2081  -1062       O  
+ATOM    438  N   GLN A  62     -16.979 -18.058 -35.515  1.00 72.21           N  
+ANISOU  438  N   GLN A  62     9647   8639   9149  -1733   1544  -1123       N  
+ATOM    439  CA  GLN A  62     -17.756 -17.359 -34.476  1.00 67.75           C  
+ANISOU  439  CA  GLN A  62     8946   8173   8619  -1633   1498  -1004       C  
+ATOM    440  C   GLN A  62     -19.164 -17.942 -34.377  1.00 73.09           C  
+ANISOU  440  C   GLN A  62     9484   8914   9371  -1894   1611  -1123       C  
+ATOM    441  O   GLN A  62     -19.705 -18.425 -35.366  1.00 70.89           O  
+ANISOU  441  O   GLN A  62     9116   8743   9073  -2166   1602  -1315       O  
+ATOM    442  CB  GLN A  62     -17.867 -15.838 -34.717  1.00 66.80           C  
+ANISOU  442  CB  GLN A  62     8639   8319   8422  -1477   1233   -915       C  
+ATOM    443  CG  GLN A  62     -19.034 -15.338 -35.614  1.00 67.21           C  
+ANISOU  443  CG  GLN A  62     8412   8696   8428  -1635   1083   -998       C  
+ATOM    444  CD  GLN A  62     -20.329 -14.964 -34.874  1.00 64.99           C  
+ANISOU  444  CD  GLN A  62     7928   8548   8214  -1649   1104   -947       C  
+ATOM    445  OE1 GLN A  62     -20.304 -14.340 -33.806  1.00 71.34           O  
+ANISOU  445  OE1 GLN A  62     8759   9285   9059  -1444   1131   -808       O  
+ATOM    446  NE2 GLN A  62     -21.471 -15.281 -35.476  1.00 63.47           N  
+ANISOU  446  NE2 GLN A  62     7516   8576   8024  -1892   1085  -1063       N  
+ATOM    447  N   SER A  63     -19.742 -17.884 -33.174  1.00 72.66           N  
+ANISOU  447  N   SER A  63     9406   8808   9392  -1819   1719  -1013       N  
+ATOM    448  CA  SER A  63     -21.142 -18.244 -32.958  1.00 72.40           C  
+ANISOU  448  CA  SER A  63     9193   8866   9449  -2039   1821  -1088       C  
+ATOM    449  C   SER A  63     -21.984 -17.121 -32.341  1.00 66.69           C  
+ANISOU  449  C   SER A  63     8251   8365   8723  -1899   1711   -963       C  
+ATOM    450  O   SER A  63     -23.178 -17.067 -32.599  1.00 77.64           O  
+ANISOU  450  O   SER A  63     9385   9960  10154  -2074   1693  -1026       O  
+ATOM    451  CB  SER A  63     -21.277 -19.527 -32.118  1.00 70.17           C  
+ANISOU  451  CB  SER A  63     9088   8272   9301  -2138   2157  -1089       C  
+ATOM    452  OG  SER A  63     -20.352 -19.523 -31.051  1.00 76.40           O  
+ANISOU  452  OG  SER A  63    10101   8853  10075  -1847   2253   -890       O  
+ATOM    453  N   PHE A  64     -21.393 -16.238 -31.540  1.00 58.38           N  
+ANISOU  453  N   PHE A  64     7282   7276   7622  -1597   1650   -796       N  
+ATOM    454  CA  PHE A  64     -22.194 -15.361 -30.713  1.00 54.39           C  
+ANISOU  454  CA  PHE A  64     6633   6895   7136  -1461   1643   -686       C  
+ATOM    455  C   PHE A  64     -23.087 -14.381 -31.501  1.00 58.70           C  
+ANISOU  455  C   PHE A  64     6865   7765   7673  -1486   1455   -693       C  
+ATOM    456  O   PHE A  64     -24.182 -14.086 -31.039  1.00 57.54           O  
+ANISOU  456  O   PHE A  64     6527   7742   7591  -1488   1516   -644       O  
+ATOM    457  CB  PHE A  64     -21.262 -14.595 -29.755  1.00 55.93           C  
+ANISOU  457  CB  PHE A  64     7010   6983   7257  -1156   1611   -549       C  
+ATOM    458  CG  PHE A  64     -21.972 -13.594 -28.871  1.00 56.33           C  
+ANISOU  458  CG  PHE A  64     6960   7132   7311   -994   1624   -455       C  
+ATOM    459  CD1 PHE A  64     -22.478 -13.970 -27.623  1.00 51.74           C  
+ANISOU  459  CD1 PHE A  64     6445   6457   6754   -951   1839   -390       C  
+ATOM    460  CD2 PHE A  64     -22.149 -12.275 -29.292  1.00 59.73           C  
+ANISOU  460  CD2 PHE A  64     7237   7734   7723   -872   1452   -423       C  
+ATOM    461  CE1 PHE A  64     -23.090 -13.031 -26.810  1.00 57.92           C  
+ANISOU  461  CE1 PHE A  64     7159   7319   7527   -791   1874   -316       C  
+ATOM    462  CE2 PHE A  64     -22.810 -11.337 -28.484  1.00 60.57           C  
+ANISOU  462  CE2 PHE A  64     7268   7898   7848   -710   1505   -344       C  
+ATOM    463  CZ  PHE A  64     -23.289 -11.715 -27.242  1.00 54.75           C  
+ANISOU  463  CZ  PHE A  64     6607   7070   7122   -674   1715   -302       C  
+ATOM    464  N   LEU A  65     -22.629 -13.842 -32.646  1.00 59.31           N  
+ANISOU  464  N   LEU A  65     6879   7987   7667  -1474   1243   -724       N  
+ATOM    465  CA  LEU A  65     -23.379 -12.775 -33.374  1.00 63.23           C  
+ANISOU  465  CA  LEU A  65     7079   8808   8137  -1426   1064   -668       C  
+ATOM    466  C   LEU A  65     -24.616 -13.283 -34.188  1.00 65.16           C  
+ANISOU  466  C   LEU A  65     7020   9342   8393  -1708   1030   -770       C  
+ATOM    467  O   LEU A  65     -24.516 -14.329 -34.834  1.00 64.66           O  
+ANISOU  467  O   LEU A  65     7003   9259   8302  -1976   1052   -946       O  
+ATOM    468  CB  LEU A  65     -22.421 -11.920 -34.276  1.00 63.03           C  
+ANISOU  468  CB  LEU A  65     7095   8842   8010  -1279    864   -623       C  
+ATOM    469  CG  LEU A  65     -21.294 -11.083 -33.600  1.00 62.01           C  
+ANISOU  469  CG  LEU A  65     7179   8506   7874  -1004    852   -518       C  
+ATOM    470  CD1 LEU A  65     -20.274 -10.486 -34.575  1.00 60.47           C  
+ANISOU  470  CD1 LEU A  65     7035   8338   7604   -917    691   -493       C  
+ATOM    471  CD2 LEU A  65     -21.842  -9.965 -32.731  1.00 60.62           C  
+ANISOU  471  CD2 LEU A  65     6923   8352   7758   -795    888   -391       C  
+ATOM    472  N   ASP A  66     -25.764 -12.554 -34.051  1.00 69.31           N  
+ANISOU  472  N   ASP A  66     7243  10123   8968  -1644    999   -661       N  
+ATOM    473  CA  ASP A  66     -27.047 -12.615 -34.848  1.00 72.82           C  
+ANISOU  473  CA  ASP A  66     7291  10968   9408  -1843    905   -692       C  
+ATOM    474  C   ASP A  66     -26.639 -12.271 -36.317  1.00 77.46           C  
+ANISOU  474  C   ASP A  66     7794  11812   9825  -1871    656   -723       C  
+ATOM    475  O   ASP A  66     -25.716 -11.438 -36.541  1.00 65.69           O  
+ANISOU  475  O   ASP A  66     6447  10241   8269  -1624    566   -617       O  
+ATOM    476  CB  ASP A  66     -28.090 -11.511 -34.364  1.00 77.64           C  
+ANISOU  476  CB  ASP A  66     7609  11789  10101  -1619    914   -476       C  
+ATOM    477  CG  ASP A  66     -29.226 -12.030 -33.407  1.00 93.62           C  
+ANISOU  477  CG  ASP A  66     9481  13808  12279  -1733   1126   -471       C  
+ATOM    478  OD1 ASP A  66     -29.080 -13.108 -32.793  1.00106.10           O  
+ANISOU  478  OD1 ASP A  66    11255  15134  13923  -1914   1308   -596       O  
+ATOM    479  OD2 ASP A  66     -30.299 -11.343 -33.266  1.00 93.76           O  
+ANISOU  479  OD2 ASP A  66     9173  14081  12368  -1624   1134   -319       O  
+ATOM    480  N   ASP A  67     -27.292 -12.872 -37.323  1.00 79.83           N  
+ANISOU  480  N   ASP A  67     7864  12428  10039  -2173    549   -870       N  
+ATOM    481  CA  ASP A  67     -26.991 -12.525 -38.711  1.00 83.48           C  
+ANISOU  481  CA  ASP A  67     8232  13188  10299  -2190    314   -888       C  
+ATOM    482  C   ASP A  67     -27.305 -11.060 -38.958  1.00 81.61           C  
+ANISOU  482  C   ASP A  67     7760  13217  10028  -1857    174   -603       C  
+ATOM    483  O   ASP A  67     -26.634 -10.428 -39.777  1.00 81.48           O  
+ANISOU  483  O   ASP A  67     7791  13288   9878  -1705     34   -521       O  
+ATOM    484  CB  ASP A  67     -27.780 -13.356 -39.743  1.00 99.82           C  
+ANISOU  484  CB  ASP A  67    10050  15632  12243  -2589    204  -1107       C  
+ATOM    485  CG  ASP A  67     -27.453 -14.842 -39.701  1.00102.82           C  
+ANISOU  485  CG  ASP A  67    10677  15732  12655  -2952    367  -1422       C  
+ATOM    486  OD1 ASP A  67     -26.299 -15.215 -39.353  1.00102.93           O  
+ANISOU  486  OD1 ASP A  67    11082  15321  12706  -2872    499  -1465       O  
+ATOM    487  OD2 ASP A  67     -28.380 -15.622 -40.029  1.00 94.69           O  
+ANISOU  487  OD2 ASP A  67     9430  14922  11623  -3321    370  -1619       O  
+ATOM    488  N   GLU A  68     -28.313 -10.508 -38.287  1.00 76.33           N  
+ANISOU  488  N   GLU A  68     6842  12669   9490  -1729    236   -436       N  
+ATOM    489  CA  GLU A  68     -28.488  -9.053 -38.331  1.00 87.60           C  
+ANISOU  489  CA  GLU A  68     8114  14233  10935  -1350    179   -137       C  
+ATOM    490  C   GLU A  68     -27.140  -8.357 -37.951  1.00 89.20           C  
+ANISOU  490  C   GLU A  68     8695  14033  11161  -1073    233    -65       C  
+ATOM    491  O   GLU A  68     -26.669  -7.443 -38.628  1.00 88.13           O  
+ANISOU  491  O   GLU A  68     8554  13978  10954   -862    128     85       O  
+ATOM    492  CB  GLU A  68     -29.608  -8.602 -37.395  1.00 95.60           C  
+ANISOU  492  CB  GLU A  68     8892  15305  12126  -1215    319     23       C  
+ATOM    493  CG  GLU A  68     -29.735  -7.087 -37.282  1.00104.83           C  
+ANISOU  493  CG  GLU A  68     9958  16515  13354   -793    334    332       C  
+ATOM    494  CD  GLU A  68     -30.926  -6.636 -36.439  1.00115.12           C  
+ANISOU  494  CD  GLU A  68    11001  17904  14832   -647    495    501       C  
+ATOM    495  OE1 GLU A  68     -31.956  -7.348 -36.393  1.00115.20           O  
+ANISOU  495  OE1 GLU A  68    10727  18166  14878   -878    505    440       O  
+ATOM    496  OE2 GLU A  68     -30.828  -5.546 -35.827  1.00115.96           O  
+ANISOU  496  OE2 GLU A  68    11189  17821  15050   -303    630    690       O  
+ATOM    497  N   GLN A  69     -26.519  -8.821 -36.871  1.00 84.99           N  
+ANISOU  497  N   GLN A  69     8479  13084  10727  -1087    401   -169       N  
+ATOM    498  CA  GLN A  69     -25.278  -8.246 -36.383  1.00 74.41           C  
+ANISOU  498  CA  GLN A  69     7470  11389   9412   -867    450   -126       C  
+ATOM    499  C   GLN A  69     -24.113  -8.417 -37.351  1.00 73.31           C  
+ANISOU  499  C   GLN A  69     7506  11209   9139   -912    323   -199       C  
+ATOM    500  O   GLN A  69     -23.352  -7.485 -37.533  1.00 68.06           O  
+ANISOU  500  O   GLN A  69     6940  10450   8469   -692    283    -80       O  
+ATOM    501  CB  GLN A  69     -24.929  -8.815 -34.993  1.00 71.55           C  
+ANISOU  501  CB  GLN A  69     7378  10660   9148   -886    645   -216       C  
+ATOM    502  CG  GLN A  69     -25.865  -8.310 -33.913  1.00 72.95           C  
+ANISOU  502  CG  GLN A  69     7442  10823   9452   -746    799   -105       C  
+ATOM    503  CD  GLN A  69     -25.579  -8.891 -32.535  1.00 72.43           C  
+ANISOU  503  CD  GLN A  69     7636  10439   9442   -758    996   -178       C  
+ATOM    504  OE1 GLN A  69     -25.227 -10.079 -32.369  1.00 64.31           O  
+ANISOU  504  OE1 GLN A  69     6765   9275   8394   -961   1053   -316       O  
+ATOM    505  NE2 GLN A  69     -25.737  -8.050 -31.530  1.00 72.76           N  
+ANISOU  505  NE2 GLN A  69     7734  10360   9548   -530   1119    -79       N  
+ATOM    506  N   ILE A  70     -23.969  -9.589 -37.964  1.00 78.29           N  
+ANISOU  506  N   ILE A  70     8181  11890   9673  -1199    285   -397       N  
+ATOM    507  CA  ILE A  70     -22.959  -9.783 -39.017  1.00 75.81           C  
+ANISOU  507  CA  ILE A  70     8009  11579   9215  -1247    178   -469       C  
+ATOM    508  C   ILE A  70     -23.247  -8.950 -40.279  1.00 80.31           C  
+ANISOU  508  C   ILE A  70     8337  12536   9640  -1154     -9   -332       C  
+ATOM    509  O   ILE A  70     -22.334  -8.336 -40.829  1.00 79.77           O  
+ANISOU  509  O   ILE A  70     8384  12414   9511   -993    -67   -242       O  
+ATOM    510  CB  ILE A  70     -22.818 -11.250 -39.409  1.00 73.74           C  
+ANISOU  510  CB  ILE A  70     7859  11274   8884  -1583    218   -732       C  
+ATOM    511  CG1 ILE A  70     -22.302 -12.031 -38.193  1.00 70.17           C  
+ANISOU  511  CG1 ILE A  70     7687  10403   8571  -1612    426   -812       C  
+ATOM    512  CG2 ILE A  70     -21.890 -11.368 -40.629  1.00 69.89           C  
+ANISOU  512  CG2 ILE A  70     7488  10843   8223  -1620    113   -800       C  
+ATOM    513  CD1 ILE A  70     -22.178 -13.529 -38.421  1.00 73.86           C  
+ANISOU  513  CD1 ILE A  70     8298  10742   9024  -1925    541  -1055       C  
+ATOM    514  N   GLY A  71     -24.501  -8.934 -40.720  1.00 80.29           N  
+ANISOU  514  N   GLY A  71     7989  12934   9582  -1249    -96   -298       N  
+ATOM    515  CA  GLY A  71     -24.945  -8.065 -41.782  1.00 84.25           C  
+ANISOU  515  CA  GLY A  71     8211  13855   9944  -1113   -267   -106       C  
+ATOM    516  C   GLY A  71     -24.627  -6.587 -41.543  1.00 90.55           C  
+ANISOU  516  C   GLY A  71     9018  14542  10843   -709   -231    194       C  
+ATOM    517  O   GLY A  71     -24.287  -5.858 -42.499  1.00 81.85           O  
+ANISOU  517  O   GLY A  71     7861  13613   9622   -547   -332    358       O  
+ATOM    518  N   GLU A  72     -24.732  -6.122 -40.290  1.00 85.84           N  
+ANISOU  518  N   GLU A  72     8502  13652  10461   -547    -67    267       N  
+ATOM    519  CA  GLU A  72     -24.363  -4.720 -39.956  1.00 84.90           C  
+ANISOU  519  CA  GLU A  72     8443  13349  10466   -189     11    507       C  
+ATOM    520  C   GLU A  72     -22.834  -4.496 -39.871  1.00 78.13           C  
+ANISOU  520  C   GLU A  72     7942  12117   9627   -119     45    456       C  
+ATOM    521  O   GLU A  72     -22.372  -3.347 -39.798  1.00 75.56           O  
+ANISOU  521  O   GLU A  72     7680  11635   9392    134    104    627       O  
+ATOM    522  CB  GLU A  72     -25.091  -4.227 -38.684  1.00 90.04           C  
+ANISOU  522  CB  GLU A  72     9044  13847  11319    -41    188    589       C  
+ATOM    523  CG  GLU A  72     -26.571  -3.883 -38.951  1.00104.52           C  
+ANISOU  523  CG  GLU A  72    10456  16088  13168     32    166    776       C  
+ATOM    524  CD  GLU A  72     -27.484  -3.868 -37.708  1.00115.41           C  
+ANISOU  524  CD  GLU A  72    11754  17371  14724     75    350    790       C  
+ATOM    525  OE1 GLU A  72     -27.080  -4.369 -36.632  1.00119.16           O  
+ANISOU  525  OE1 GLU A  72    12496  17503  15276    -13    480    617       O  
+ATOM    526  OE2 GLU A  72     -28.638  -3.366 -37.807  1.00117.96           O  
+ANISOU  526  OE2 GLU A  72    11730  17986  15102    210    373    993       O  
+ATOM    527  N   GLY A  73     -22.058  -5.585 -39.875  1.00 67.33           N  
+ANISOU  527  N   GLY A  73     6793  10600   8189   -345     28    226       N  
+ATOM    528  CA  GLY A  73     -20.599  -5.498 -39.918  1.00 67.28           C  
+ANISOU  528  CA  GLY A  73     7077  10299   8185   -298     44    183       C  
+ATOM    529  C   GLY A  73     -19.821  -5.908 -38.667  1.00 62.16           C  
+ANISOU  529  C   GLY A  73     6708   9260   7648   -326    164     53       C  
+ATOM    530  O   GLY A  73     -18.585  -5.771 -38.638  1.00 63.30           O  
+ANISOU  530  O   GLY A  73     7062   9181   7806   -276    171     35       O  
+ATOM    531  N   PHE A  74     -20.506  -6.407 -37.635  1.00 54.21           N  
+ANISOU  531  N   PHE A  74     5695   8188   6714   -400    259    -21       N  
+ATOM    532  CA  PHE A  74     -19.813  -6.733 -36.379  1.00 50.47           C  
+ANISOU  532  CA  PHE A  74     5476   7384   6317   -394    373   -110       C  
+ATOM    533  C   PHE A  74     -19.017  -7.976 -36.610  1.00 48.37           C  
+ANISOU  533  C   PHE A  74     5385   7015   5978   -577    371   -263       C  
+ATOM    534  O   PHE A  74     -19.389  -8.786 -37.447  1.00 48.97           O  
+ANISOU  534  O   PHE A  74     5379   7259   5968   -764    327   -353       O  
+ATOM    535  CB  PHE A  74     -20.762  -6.849 -35.179  1.00 51.93           C  
+ANISOU  535  CB  PHE A  74     5616   7527   6587   -388    503   -119       C  
+ATOM    536  CG  PHE A  74     -21.382  -5.561 -34.825  1.00 54.65           C  
+ANISOU  536  CG  PHE A  74     5836   7903   7023   -170    553     31       C  
+ATOM    537  CD1 PHE A  74     -20.611  -4.556 -34.263  1.00 59.00           C  
+ANISOU  537  CD1 PHE A  74     6552   8226   7638     12    602     74       C  
+ATOM    538  CD2 PHE A  74     -22.705  -5.309 -35.097  1.00 62.03           C  
+ANISOU  538  CD2 PHE A  74     6482   9097   7988   -145    562    133       C  
+ATOM    539  CE1 PHE A  74     -21.141  -3.312 -33.970  1.00 61.30           C  
+ANISOU  539  CE1 PHE A  74     6759   8497   8034    221    689    205       C  
+ATOM    540  CE2 PHE A  74     -23.278  -4.074 -34.762  1.00 65.97           C  
+ANISOU  540  CE2 PHE A  74     6870   9599   8593     96    649    300       C  
+ATOM    541  CZ  PHE A  74     -22.481  -3.064 -34.213  1.00 69.36           C  
+ANISOU  541  CZ  PHE A  74     7503   9751   9097    283    726    331       C  
+ATOM    542  N   VAL A  75     -17.889  -8.074 -35.901  1.00 48.27           N  
+ANISOU  542  N   VAL A  75     5608   6737   5995   -517    420   -290       N  
+ATOM    543  CA  VAL A  75     -16.947  -9.203 -35.999  1.00 47.38           C  
+ANISOU  543  CA  VAL A  75     5685   6480   5837   -632    453   -395       C  
+ATOM    544  C   VAL A  75     -16.430  -9.520 -34.615  1.00 49.15           C  
+ANISOU  544  C   VAL A  75     6091   6473   6108   -575    558   -404       C  
+ATOM    545  O   VAL A  75     -16.248  -8.629 -33.798  1.00 47.13           O  
+ANISOU  545  O   VAL A  75     5866   6148   5892   -428    559   -343       O  
+ATOM    546  CB  VAL A  75     -15.775  -8.834 -36.956  1.00 48.33           C  
+ANISOU  546  CB  VAL A  75     5867   6583   5911   -571    365   -359       C  
+ATOM    547  CG1 VAL A  75     -15.079  -7.549 -36.507  1.00 49.98           C  
+ANISOU  547  CG1 VAL A  75     6112   6686   6192   -372    333   -248       C  
+ATOM    548  CG2 VAL A  75     -14.782  -9.929 -37.088  1.00 49.25           C  
+ANISOU  548  CG2 VAL A  75     6167   6549   5995   -653    422   -442       C  
+ATOM    549  N   LEU A  76     -16.184 -10.794 -34.355  1.00 49.57           N  
+ANISOU  549  N   LEU A  76     6273   6411   6149   -688    660   -479       N  
+ATOM    550  CA  LEU A  76     -15.521 -11.198 -33.153  1.00 47.93           C  
+ANISOU  550  CA  LEU A  76     6243   6013   5953   -611    755   -452       C  
+ATOM    551  C   LEU A  76     -14.098 -11.431 -33.507  1.00 45.41           C  
+ANISOU  551  C   LEU A  76     6054   5590   5609   -559    721   -432       C  
+ATOM    552  O   LEU A  76     -13.751 -12.422 -34.211  1.00 46.04           O  
+ANISOU  552  O   LEU A  76     6200   5615   5676   -659    783   -486       O  
+ATOM    553  CB  LEU A  76     -16.177 -12.472 -32.551  1.00 49.85           C  
+ANISOU  553  CB  LEU A  76     6545   6174   6220   -737    935   -501       C  
+ATOM    554  CG  LEU A  76     -17.619 -12.228 -32.105  1.00 52.45           C  
+ANISOU  554  CG  LEU A  76     6721   6616   6591   -787    985   -507       C  
+ATOM    555  CD1 LEU A  76     -18.258 -13.483 -31.561  1.00 56.78           C  
+ANISOU  555  CD1 LEU A  76     7318   7068   7185   -930   1185   -551       C  
+ATOM    556  CD2 LEU A  76     -17.640 -11.190 -31.039  1.00 52.12           C  
+ANISOU  556  CD2 LEU A  76     6691   6565   6545   -599    972   -426       C  
+ATOM    557  N   THR A  77     -13.248 -10.565 -32.967  1.00 46.19           N  
+ANISOU  557  N   THR A  77     6193   5650   5705   -409    646   -365       N  
+ATOM    558  CA  THR A  77     -11.875 -10.505 -33.442  1.00 42.15           C  
+ANISOU  558  CA  THR A  77     5743   5084   5186   -350    586   -327       C  
+ATOM    559  C   THR A  77     -11.098 -11.716 -33.100  1.00 45.26           C  
+ANISOU  559  C   THR A  77     6277   5354   5565   -343    692   -303       C  
+ATOM    560  O   THR A  77     -10.095 -11.997 -33.772  1.00 50.56           O  
+ANISOU  560  O   THR A  77     6987   5982   6241   -320    686   -277       O  
+ATOM    561  CB  THR A  77     -11.139  -9.239 -32.928  1.00 47.57           C  
+ANISOU  561  CB  THR A  77     6417   5768   5889   -225    479   -279       C  
+ATOM    562  OG1 THR A  77     -11.277  -9.041 -31.498  1.00 46.78           O  
+ANISOU  562  OG1 THR A  77     6374   5641   5757   -165    507   -279       O  
+ATOM    563  CG2 THR A  77     -11.677  -8.033 -33.637  1.00 44.69           C  
+ANISOU  563  CG2 THR A  77     5923   5486   5568   -210    405   -272       C  
+ATOM    564  N   CYS A  78     -11.496 -12.435 -32.033  1.00 50.28           N  
+ANISOU  564  N   CYS A  78     6990   5924   6188   -338    814   -286       N  
+ATOM    565  CA  CYS A  78     -10.739 -13.646 -31.587  1.00 46.96           C  
+ANISOU  565  CA  CYS A  78     6711   5367   5761   -289    955   -214       C  
+ATOM    566  C   CYS A  78     -11.053 -14.787 -32.559  1.00 49.46           C  
+ANISOU  566  C   CYS A  78     7079   5587   6126   -435   1104   -293       C  
+ATOM    567  O   CYS A  78     -10.411 -15.828 -32.559  1.00 51.48           O  
+ANISOU  567  O   CYS A  78     7458   5693   6407   -405   1257   -244       O  
+ATOM    568  CB  CYS A  78     -11.178 -14.092 -30.182  1.00 53.40           C  
+ANISOU  568  CB  CYS A  78     7600   6145   6541   -234   1071   -151       C  
+ATOM    569  SG  CYS A  78     -12.881 -14.758 -30.242  1.00 51.94           S  
+ANISOU  569  SG  CYS A  78     7387   5928   6417   -420   1238   -249       S  
+ATOM    570  N   ALA A  79     -12.058 -14.598 -33.405  1.00 53.34           N  
+ANISOU  570  N   ALA A  79     7469   6170   6626   -598   1068   -418       N  
+ATOM    571  CA  ALA A  79     -12.515 -15.685 -34.236  1.00 55.83           C  
+ANISOU  571  CA  ALA A  79     7829   6416   6967   -787   1210   -543       C  
+ATOM    572  C   ALA A  79     -12.550 -15.316 -35.744  1.00 59.35           C  
+ANISOU  572  C   ALA A  79     8188   7002   7360   -894   1092   -650       C  
+ATOM    573  O   ALA A  79     -13.139 -16.061 -36.535  1.00 55.41           O  
+ANISOU  573  O   ALA A  79     7693   6513   6847  -1099   1172   -802       O  
+ATOM    574  CB  ALA A  79     -13.912 -16.109 -33.759  1.00 59.21           C  
+ANISOU  574  CB  ALA A  79     8205   6858   7433   -940   1313   -616       C  
+ATOM    575  N   ALA A  80     -11.913 -14.208 -36.131  1.00 51.54           N  
+ANISOU  575  N   ALA A  80     7126   6121   6335   -767    917   -576       N  
+ATOM    576  CA  ALA A  80     -12.025 -13.689 -37.496  1.00 52.60           C  
+ANISOU  576  CA  ALA A  80     7161   6426   6398   -833    799   -635       C  
+ATOM    577  C   ALA A  80     -10.641 -13.659 -38.187  1.00 52.00           C  
+ANISOU  577  C   ALA A  80     7168   6282   6305   -734    797   -581       C  
+ATOM    578  O   ALA A  80      -9.618 -13.161 -37.620  1.00 49.22           O  
+ANISOU  578  O   ALA A  80     6840   5858   6002   -561    760   -450       O  
+ATOM    579  CB  ALA A  80     -12.672 -12.314 -37.499  1.00 53.13           C  
+ANISOU  579  CB  ALA A  80     7044   6690   6453   -769    627   -571       C  
+ATOM    580  N   TYR A  81     -10.617 -14.269 -39.382  1.00 50.25           N  
+ANISOU  580  N   TYR A  81     6991   6091   6011   -860    853   -698       N  
+ATOM    581  CA  TYR A  81      -9.473 -14.232 -40.301  1.00 47.17           C  
+ANISOU  581  CA  TYR A  81     6664   5673   5582   -786    868   -665       C  
+ATOM    582  C   TYR A  81      -9.695 -13.111 -41.287  1.00 50.29           C  
+ANISOU  582  C   TYR A  81     6913   6311   5882   -771    694   -634       C  
+ATOM    583  O   TYR A  81     -10.787 -12.986 -41.832  1.00 51.07           O  
+ANISOU  583  O   TYR A  81     6906   6613   5885   -903    620   -722       O  
+ATOM    584  CB  TYR A  81      -9.426 -15.493 -41.146  1.00 51.08           C  
+ANISOU  584  CB  TYR A  81     7306   6080   6021   -943   1048   -833       C  
+ATOM    585  CG  TYR A  81      -9.189 -16.735 -40.354  1.00 58.36           C  
+ANISOU  585  CG  TYR A  81     8398   6724   7050   -954   1282   -854       C  
+ATOM    586  CD1 TYR A  81      -8.089 -16.833 -39.537  1.00 55.81           C  
+ANISOU  586  CD1 TYR A  81     8143   6231   6829   -740   1353   -672       C  
+ATOM    587  CD2 TYR A  81     -10.088 -17.800 -40.389  1.00 63.94           C  
+ANISOU  587  CD2 TYR A  81     9183   7347   7763  -1179   1441  -1042       C  
+ATOM    588  CE1 TYR A  81      -7.853 -17.958 -38.801  1.00 58.92           C  
+ANISOU  588  CE1 TYR A  81     8687   6381   7317   -708   1583   -641       C  
+ATOM    589  CE2 TYR A  81      -9.854 -18.945 -39.642  1.00 66.35           C  
+ANISOU  589  CE2 TYR A  81     9659   7359   8190  -1168   1700  -1029       C  
+ATOM    590  CZ  TYR A  81      -8.713 -19.009 -38.869  1.00 60.72           C  
+ANISOU  590  CZ  TYR A  81     9018   6485   7566   -910   1772   -810       C  
+ATOM    591  OH  TYR A  81      -8.409 -20.106 -38.119  1.00 67.42           O  
+ANISOU  591  OH  TYR A  81    10026   7058   8530   -846   2038   -740       O  
+ATOM    592  N   PRO A  82      -8.665 -12.297 -41.547  1.00 49.08           N  
+ANISOU  592  N   PRO A  82     6740   6152   5756   -609    636   -494       N  
+ATOM    593  CA  PRO A  82      -8.810 -11.345 -42.651  1.00 47.57           C  
+ANISOU  593  CA  PRO A  82     6433   6172   5466   -585    518   -444       C  
+ATOM    594  C   PRO A  82      -8.910 -12.091 -43.994  1.00 51.19           C  
+ANISOU  594  C   PRO A  82     6956   6741   5751   -719    580   -581       C  
+ATOM    595  O   PRO A  82      -8.241 -13.098 -44.143  1.00 50.40           O  
+ANISOU  595  O   PRO A  82     7018   6474   5657   -755    739   -662       O  
+ATOM    596  CB  PRO A  82      -7.518 -10.563 -42.588  1.00 45.77           C  
+ANISOU  596  CB  PRO A  82     6205   5851   5335   -407    504   -279       C  
+ATOM    597  CG  PRO A  82      -6.511 -11.495 -41.974  1.00 47.02           C  
+ANISOU  597  CG  PRO A  82     6497   5788   5579   -368    638   -280       C  
+ATOM    598  CD  PRO A  82      -7.288 -12.383 -41.033  1.00 48.95           C  
+ANISOU  598  CD  PRO A  82     6803   5951   5844   -460    702   -380       C  
+ATOM    599  N   THR A  83      -9.757 -11.627 -44.924  1.00 48.49           N  
+ANISOU  599  N   THR A  83     6489   6685   5247   -788    466   -606       N  
+ATOM    600  CA  THR A  83      -9.762 -12.153 -46.307  1.00 51.50           C  
+ANISOU  600  CA  THR A  83     6925   7231   5411   -907    499   -734       C  
+ATOM    601  C   THR A  83      -9.429 -11.095 -47.342  1.00 49.00           C  
+ANISOU  601  C   THR A  83     6517   7124   4975   -771    406   -571       C  
+ATOM    602  O   THR A  83      -9.557 -11.323 -48.533  1.00 50.94           O  
+ANISOU  602  O   THR A  83     6777   7584   4992   -851    400   -650       O  
+ATOM    603  CB  THR A  83     -11.157 -12.749 -46.647  1.00 56.46           C  
+ANISOU  603  CB  THR A  83     7475   8093   5884  -1158    444   -940       C  
+ATOM    604  OG1 THR A  83     -12.178 -11.809 -46.291  1.00 57.08           O  
+ANISOU  604  OG1 THR A  83     7322   8384   5979  -1111    275   -821       O  
+ATOM    605  CG2 THR A  83     -11.377 -14.007 -45.846  1.00 57.41           C  
+ANISOU  605  CG2 THR A  83     7729   7967   6115  -1324    602  -1126       C  
+ATOM    606  N   SER A  84      -9.123  -9.892 -46.868  1.00 49.80           N  
+ANISOU  606  N   SER A  84     6516   7183   5220   -575    335   -345       N  
+ATOM    607  CA  SER A  84      -8.642  -8.809 -47.689  1.00 51.09           C  
+ANISOU  607  CA  SER A  84     6609   7464   5339   -413    295   -145       C  
+ATOM    608  C   SER A  84      -8.017  -7.870 -46.668  1.00 49.54           C  
+ANISOU  608  C   SER A  84     6376   7040   5405   -251    294     24       C  
+ATOM    609  O   SER A  84      -8.128  -8.093 -45.490  1.00 47.99           O  
+ANISOU  609  O   SER A  84     6201   6679   5354   -276    298    -28       O  
+ATOM    610  CB  SER A  84      -9.795  -8.069 -48.389  1.00 56.08           C  
+ANISOU  610  CB  SER A  84     7050   8454   5800   -400    154    -60       C  
+ATOM    611  OG  SER A  84     -10.589  -7.330 -47.413  1.00 52.75           O  
+ANISOU  611  OG  SER A  84     6487   8017   5536   -337     76     32       O  
+ATOM    612  N   ASP A  85      -7.382  -6.806 -47.126  1.00 46.38           N  
+ANISOU  612  N   ASP A  85     5924   6639   5057    -96    299    222       N  
+ATOM    613  CA  ASP A  85      -6.983  -5.755 -46.253  1.00 49.05           C  
+ANISOU  613  CA  ASP A  85     6206   6797   5631     21    291    358       C  
+ATOM    614  C   ASP A  85      -8.286  -5.304 -45.638  1.00 50.62           C  
+ANISOU  614  C   ASP A  85     6295   7088   5849     14    202    357       C  
+ATOM    615  O   ASP A  85      -9.334  -5.212 -46.322  1.00 54.44           O  
+ANISOU  615  O   ASP A  85     6675   7839   6170      0    136    381       O  
+ATOM    616  CB  ASP A  85      -6.341  -4.609 -47.058  1.00 47.60           C  
+ANISOU  616  CB  ASP A  85     5967   6628   5489    170    330    579       C  
+ATOM    617  CG  ASP A  85      -4.900  -4.925 -47.559  1.00 52.73           C  
+ANISOU  617  CG  ASP A  85     6707   7157   6169    197    442    609       C  
+ATOM    618  OD1 ASP A  85      -4.277  -5.936 -47.150  1.00 52.35           O  
+ANISOU  618  OD1 ASP A  85     6760   6983   6148    128    494    481       O  
+ATOM    619  OD2 ASP A  85      -4.368  -4.108 -48.369  1.00 56.01           O  
+ANISOU  619  OD2 ASP A  85     7082   7598   6598    307    501    791       O  
+ATOM    620  N   VAL A  86      -8.255  -4.968 -44.377  1.00 45.98           N  
+ANISOU  620  N   VAL A  86     5710   6311   5446     32    200    343       N  
+ATOM    621  CA  VAL A  86      -9.522  -4.737 -43.682  1.00 45.59           C  
+ANISOU  621  CA  VAL A  86     5573   6331   5415     18    147    316       C  
+ATOM    622  C   VAL A  86      -9.338  -3.725 -42.597  1.00 43.07           C  
+ANISOU  622  C   VAL A  86     5245   5812   5305    107    169    375       C  
+ATOM    623  O   VAL A  86      -8.275  -3.619 -42.020  1.00 44.22           O  
+ANISOU  623  O   VAL A  86     5470   5760   5572    112    201    355       O  
+ATOM    624  CB  VAL A  86     -10.078  -6.072 -43.148  1.00 48.01           C  
+ANISOU  624  CB  VAL A  86     5939   6654   5647   -143    144    117       C  
+ATOM    625  CG1 VAL A  86      -9.082  -6.710 -42.219  1.00 49.95           C  
+ANISOU  625  CG1 VAL A  86     6328   6652   5997   -170    206     38       C  
+ATOM    626  CG2 VAL A  86     -11.442  -5.939 -42.465  1.00 50.17           C  
+ANISOU  626  CG2 VAL A  86     6107   7020   5936   -171    105     89       C  
+ATOM    627  N   THR A  87     -10.371  -2.925 -42.367  1.00 45.19           N  
+ANISOU  627  N   THR A  87     5406   6148   5615    181    159    451       N  
+ATOM    628  CA  THR A  87     -10.350  -1.923 -41.352  1.00 45.50           C  
+ANISOU  628  CA  THR A  87     5452   5991   5845    259    209    481       C  
+ATOM    629  C   THR A  87     -11.421  -2.288 -40.351  1.00 47.74           C  
+ANISOU  629  C   THR A  87     5716   6302   6122    213    199    378       C  
+ATOM    630  O   THR A  87     -12.526  -2.582 -40.730  1.00 47.10           O  
+ANISOU  630  O   THR A  87     5523   6431   5940    201    166    397       O  
+ATOM    631  CB  THR A  87     -10.656  -0.544 -41.917  1.00 50.80           C  
+ANISOU  631  CB  THR A  87     6025   6671   6605    425    268    690       C  
+ATOM    632  OG1 THR A  87      -9.617  -0.209 -42.839  1.00 51.07           O  
+ANISOU  632  OG1 THR A  87     6082   6667   6653    467    301    799       O  
+ATOM    633  CG2 THR A  87     -10.675   0.502 -40.782  1.00 50.21           C  
+ANISOU  633  CG2 THR A  87     5986   6346   6744    486    359    679       C  
+ATOM    634  N   ILE A  88     -11.062  -2.273 -39.075  1.00 47.12           N  
+ANISOU  634  N   ILE A  88     5735   6028   6137    183    227    271       N  
+ATOM    635  CA  ILE A  88     -11.915  -2.724 -38.016  1.00 47.67           C  
+ANISOU  635  CA  ILE A  88     5818   6102   6192    138    240    168       C  
+ATOM    636  C   ILE A  88     -11.927  -1.719 -36.867  1.00 42.11           C  
+ANISOU  636  C   ILE A  88     5161   5214   5622    206    309    145       C  
+ATOM    637  O   ILE A  88     -10.907  -1.494 -36.286  1.00 43.07           O  
+ANISOU  637  O   ILE A  88     5383   5181   5801    181    309     80       O  
+ATOM    638  CB  ILE A  88     -11.395  -4.068 -37.512  1.00 49.90           C  
+ANISOU  638  CB  ILE A  88     6214   6349   6396     13    220     34       C  
+ATOM    639  CG1 ILE A  88     -11.587  -5.112 -38.628  1.00 49.65           C  
+ANISOU  639  CG1 ILE A  88     6153   6480   6231    -76    191     16       C  
+ATOM    640  CG2 ILE A  88     -12.108  -4.473 -36.212  1.00 51.61           C  
+ANISOU  640  CG2 ILE A  88     6470   6528   6608    -19    261    -58       C  
+ATOM    641  CD1 ILE A  88     -10.896  -6.432 -38.386  1.00 49.71           C  
+ANISOU  641  CD1 ILE A  88     6291   6410   6186   -176    218    -87       C  
+ATOM    642  N   GLU A  89     -13.099  -1.193 -36.519  1.00 43.90           N  
+ANISOU  642  N   GLU A  89     5312   5478   5890    282    372    184       N  
+ATOM    643  CA  GLU A  89     -13.278  -0.421 -35.290  1.00 47.43           C  
+ANISOU  643  CA  GLU A  89     5831   5749   6437    331    467    118       C  
+ATOM    644  C   GLU A  89     -13.369  -1.368 -34.118  1.00 48.10           C  
+ANISOU  644  C   GLU A  89     6014   5828   6434    235    456    -33       C  
+ATOM    645  O   GLU A  89     -14.208  -2.238 -34.131  1.00 46.09           O  
+ANISOU  645  O   GLU A  89     5699   5711   6099    192    450    -38       O  
+ATOM    646  CB  GLU A  89     -14.570   0.378 -35.316  1.00 52.55           C  
+ANISOU  646  CB  GLU A  89     6361   6442   7161    470    572    230       C  
+ATOM    647  CG  GLU A  89     -14.633   1.492 -36.347  1.00 63.41           C  
+ANISOU  647  CG  GLU A  89     7637   7813   8643    621    629    431       C  
+ATOM    648  CD  GLU A  89     -15.842   2.407 -36.147  1.00 73.77           C  
+ANISOU  648  CD  GLU A  89     8843   9123  10063    800    777    562       C  
+ATOM    649  OE1 GLU A  89     -16.733   2.070 -35.336  1.00 80.53           O  
+ANISOU  649  OE1 GLU A  89     9673  10027  10895    795    819    497       O  
+ATOM    650  OE2 GLU A  89     -15.887   3.472 -36.793  1.00 76.86           O  
+ANISOU  650  OE2 GLU A  89     9175   9453  10575    962    875    747       O  
+ATOM    651  N   THR A  90     -12.531  -1.166 -33.102  1.00 44.70           N  
+ANISOU  651  N   THR A  90     5722   5248   6013    199    462   -150       N  
+ATOM    652  CA  THR A  90     -12.427  -2.084 -32.002  1.00 43.34           C  
+ANISOU  652  CA  THR A  90     5650   5087   5727    129    448   -262       C  
+ATOM    653  C   THR A  90     -13.337  -1.652 -30.827  1.00 47.39           C  
+ANISOU  653  C   THR A  90     6210   5556   6240    178    561   -329       C  
+ATOM    654  O   THR A  90     -13.940  -0.586 -30.855  1.00 46.89           O  
+ANISOU  654  O   THR A  90     6109   5423   6283    268    659   -299       O  
+ATOM    655  CB  THR A  90     -10.937  -2.167 -31.551  1.00 42.54           C  
+ANISOU  655  CB  THR A  90     5651   4917   5596     69    368   -337       C  
+ATOM    656  OG1 THR A  90     -10.480  -0.884 -31.081  1.00 46.16           O  
+ANISOU  656  OG1 THR A  90     6155   5238   6145     78    400   -410       O  
+ATOM    657  CG2 THR A  90     -10.008  -2.601 -32.693  1.00 42.77           C  
+ANISOU  657  CG2 THR A  90     5633   4980   5636     38    287   -260       C  
+ATOM    658  N   HIS A  91     -13.394  -2.452 -29.757  1.00 47.53           N  
+ANISOU  658  N   HIS A  91     6321   5601   6138    136    573   -409       N  
+ATOM    659  CA  HIS A  91     -14.121  -2.027 -28.523  1.00 50.54           C  
+ANISOU  659  CA  HIS A  91     6775   5936   6488    184    696   -488       C  
+ATOM    660  C   HIS A  91     -15.577  -1.689 -28.823  1.00 48.63           C  
+ANISOU  660  C   HIS A  91     6407   5732   6336    269    818   -403       C  
+ATOM    661  O   HIS A  91     -16.087  -0.683 -28.370  1.00 47.55           O  
+ANISOU  661  O   HIS A  91     6289   5503   6273    358    945   -426       O  
+ATOM    662  CB  HIS A  91     -13.449  -0.819 -27.839  1.00 53.09           C  
+ANISOU  662  CB  HIS A  91     7212   6116   6841    192    723   -613       C  
+ATOM    663  CG  HIS A  91     -12.037  -1.062 -27.377  1.00 53.84           C  
+ANISOU  663  CG  HIS A  91     7400   6222   6835     99    592   -706       C  
+ATOM    664  ND1 HIS A  91     -10.998  -1.282 -28.245  1.00 52.95           N  
+ANISOU  664  ND1 HIS A  91     7230   6124   6762     50    467   -650       N  
+ATOM    665  CD2 HIS A  91     -11.494  -1.106 -26.132  1.00 56.62           C  
+ANISOU  665  CD2 HIS A  91     7877   6601   7033     54    565   -841       C  
+ATOM    666  CE1 HIS A  91      -9.869  -1.434 -27.568  1.00 52.38           C  
+ANISOU  666  CE1 HIS A  91     7223   6088   6589    -18    367   -735       C  
+ATOM    667  NE2 HIS A  91     -10.149  -1.348 -26.282  1.00 55.87           N  
+ANISOU  667  NE2 HIS A  91     7774   6556   6899    -20    411   -852       N  
+ATOM    668  N   LYS A  92     -16.228  -2.521 -29.624  1.00 49.04           N  
+ANISOU  668  N   LYS A  92     6318   5927   6386    236    787   -308       N  
+ATOM    669  CA  LYS A  92     -17.650  -2.390 -29.844  1.00 50.58           C  
+ANISOU  669  CA  LYS A  92     6348   6224   6644    297    884   -219       C  
+ATOM    670  C   LYS A  92     -18.507  -3.326 -28.988  1.00 47.54           C  
+ANISOU  670  C   LYS A  92     5964   5904   6193    250    976   -250       C  
+ATOM    671  O   LYS A  92     -19.654  -3.503 -29.328  1.00 46.77           O  
+ANISOU  671  O   LYS A  92     5686   5937   6144    257   1030   -172       O  
+ATOM    672  CB  LYS A  92     -17.947  -2.701 -31.306  1.00 53.04           C  
+ANISOU  672  CB  LYS A  92     6468   6705   6979    263    785   -107       C  
+ATOM    673  CG  LYS A  92     -17.183  -1.817 -32.271  1.00 56.58           C  
+ANISOU  673  CG  LYS A  92     6898   7107   7489    325    715    -36       C  
+ATOM    674  CD  LYS A  92     -17.486  -0.352 -32.061  1.00 58.78           C  
+ANISOU  674  CD  LYS A  92     7167   7262   7905    494    841     28       C  
+ATOM    675  CE  LYS A  92     -18.585   0.113 -32.975  1.00 67.73           C  
+ANISOU  675  CE  LYS A  92     8061   8564   9107    618    876    223       C  
+ATOM    676  NZ  LYS A  92     -18.423   1.591 -33.141  1.00 70.69           N  
+ANISOU  676  NZ  LYS A  92     8453   8766   9637    795    997    324       N  
+ATOM    677  N   GLU A  93     -17.977  -3.940 -27.920  1.00 48.14           N  
+ANISOU  677  N   GLU A  93     6220   5912   6155    204    998   -342       N  
+ATOM    678  CA  GLU A  93     -18.834  -4.744 -26.990  1.00 51.58           C  
+ANISOU  678  CA  GLU A  93     6674   6388   6535    183   1133   -348       C  
+ATOM    679  C   GLU A  93     -20.133  -4.043 -26.630  1.00 53.52           C  
+ANISOU  679  C   GLU A  93     6808   6660   6864    287   1296   -305       C  
+ATOM    680  O   GLU A  93     -21.165  -4.650 -26.637  1.00 58.70           O  
+ANISOU  680  O   GLU A  93     7330   7419   7554    250   1380   -249       O  
+ATOM    681  CB  GLU A  93     -18.112  -5.078 -25.684  1.00 53.98           C  
+ANISOU  681  CB  GLU A  93     7203   6619   6686    189   1166   -429       C  
+ATOM    682  CG  GLU A  93     -18.999  -5.656 -24.586  1.00 58.34           C  
+ANISOU  682  CG  GLU A  93     7798   7194   7171    208   1345   -418       C  
+ATOM    683  CD  GLU A  93     -18.194  -6.346 -23.498  1.00 59.78           C  
+ANISOU  683  CD  GLU A  93     8187   7360   7166    207   1352   -449       C  
+ATOM    684  OE1 GLU A  93     -17.556  -5.652 -22.668  1.00 64.37           O  
+ANISOU  684  OE1 GLU A  93     8915   7917   7626    267   1330   -538       O  
+ATOM    685  OE2 GLU A  93     -18.184  -7.597 -23.528  1.00 52.88           O  
+ANISOU  685  OE2 GLU A  93     7321   6504   6265    142   1381   -382       O  
+ATOM    686  N   GLU A  94     -20.084  -2.768 -26.311  1.00 59.72           N  
+ANISOU  686  N   GLU A  94     7647   7342   7699    413   1362   -331       N  
+ATOM    687  CA  GLU A  94     -21.265  -2.097 -25.790  1.00 66.89           C  
+ANISOU  687  CA  GLU A  94     8483   8242   8687    544   1565   -289       C  
+ATOM    688  C   GLU A  94     -22.389  -2.061 -26.822  1.00 70.98           C  
+ANISOU  688  C   GLU A  94     8697   8926   9344    581   1575   -124       C  
+ATOM    689  O   GLU A  94     -23.572  -2.215 -26.481  1.00 76.40           O  
+ANISOU  689  O   GLU A  94     9243   9704  10081    626   1721    -54       O  
+ATOM    690  CB  GLU A  94     -20.887  -0.700 -25.315  1.00 74.24           C  
+ANISOU  690  CB  GLU A  94     9560   8986   9660    665   1660   -370       C  
+ATOM    691  CG  GLU A  94     -20.302  -0.701 -23.891  1.00 88.53           C  
+ANISOU  691  CG  GLU A  94    11642  10696  11297    640   1723   -551       C  
+ATOM    692  CD  GLU A  94     -21.356  -0.505 -22.760  1.00104.83           C  
+ANISOU  692  CD  GLU A  94    13759  12740  13331    745   1979   -573       C  
+ATOM    693  OE1 GLU A  94     -20.982   0.024 -21.666  1.00102.89           O  
+ANISOU  693  OE1 GLU A  94    13744  12388  12962    767   2076   -740       O  
+ATOM    694  OE2 GLU A  94     -22.562  -0.867 -22.947  1.00106.29           O  
+ANISOU  694  OE2 GLU A  94    13749  13029  13605    797   2092   -434       O  
+ATOM    695  N   ALA A  95     -22.007  -1.909 -28.091  1.00 68.41           N  
+ANISOU  695  N   ALA A  95     8255   8672   9065    556   1414    -53       N  
+ATOM    696  CA  ALA A  95     -22.956  -1.709 -29.182  1.00 66.09           C  
+ANISOU  696  CA  ALA A  95     7658   8583   8869    608   1388    116       C  
+ATOM    697  C   ALA A  95     -23.662  -2.996 -29.528  1.00 66.44           C  
+ANISOU  697  C   ALA A  95     7523   8851   8867    435   1328    127       C  
+ATOM    698  O   ALA A  95     -24.779  -2.940 -30.017  1.00 70.13           O  
+ANISOU  698  O   ALA A  95     7710   9533   9402    465   1352    251       O  
+ATOM    699  CB  ALA A  95     -22.245  -1.163 -30.422  1.00 66.10           C  
+ANISOU  699  CB  ALA A  95     7613   8606   8896    636   1238    189       C  
+ATOM    700  N   ILE A  96     -23.008  -4.142 -29.324  1.00 64.35           N  
+ANISOU  700  N   ILE A  96     7407   8544   8498    253   1257      4       N  
+ATOM    701  CA  ILE A  96     -23.650  -5.436 -29.582  1.00 69.19           C  
+ANISOU  701  CA  ILE A  96     7886   9314   9088     56   1244    -17       C  
+ATOM    702  C   ILE A  96     -24.290  -6.032 -28.311  1.00 75.00           C  
+ANISOU  702  C   ILE A  96     8682   9987   9825     30   1440    -50       C  
+ATOM    703  O   ILE A  96     -24.815  -7.127 -28.332  1.00 68.54           O  
+ANISOU  703  O   ILE A  96     7782   9246   9011   -142   1479    -77       O  
+ATOM    704  CB  ILE A  96     -22.743  -6.492 -30.279  1.00 69.26           C  
+ANISOU  704  CB  ILE A  96     7991   9314   9009   -136   1099   -110       C  
+ATOM    705  CG1 ILE A  96     -21.443  -6.740 -29.528  1.00 72.23           C  
+ANISOU  705  CG1 ILE A  96     8677   9458   9305   -123   1101   -195       C  
+ATOM    706  CG2 ILE A  96     -22.463  -6.154 -31.716  1.00 67.05           C  
+ANISOU  706  CG2 ILE A  96     7581   9181   8715   -151    922    -66       C  
+ATOM    707  CD1 ILE A  96     -21.463  -8.031 -28.757  1.00 71.63           C  
+ANISOU  707  CD1 ILE A  96     8723   9309   9184   -245   1210   -253       C  
+ATOM    708  N   MET A  97     -24.258  -5.310 -27.201  1.00 82.61           N  
+ANISOU  708  N   MET A  97     9796  10805  10784    194   1584    -55       N  
+ATOM    709  CA  MET A  97     -25.147  -5.636 -26.099  1.00 87.11           C  
+ANISOU  709  CA  MET A  97    10364  11365  11366    215   1801    -42       C  
+ATOM    710  C   MET A  97     -26.325  -4.668 -26.205  1.00 95.61           C  
+ANISOU  710  C   MET A  97    11196  12551  12577    376   1919     80       C  
+ATOM    711  O   MET A  97     -27.410  -5.101 -26.587  1.00 94.92           O  
+ANISOU  711  O   MET A  97    10826  12664  12575    303   1954    163       O  
+ATOM    712  CB  MET A  97     -24.435  -5.516 -24.761  1.00 78.92           C  
+ANISOU  712  CB  MET A  97     9648  10134  10203    296   1904   -129       C  
+ATOM    713  CG  MET A  97     -23.264  -6.468 -24.547  1.00 69.75           C  
+ANISOU  713  CG  MET A  97     8709   8888   8904    181   1804   -207       C  
+ATOM    714  SD  MET A  97     -22.432  -5.914 -23.038  1.00 73.23           S  
+ANISOU  714  SD  MET A  97     9478   9183   9162    316   1882   -298       S  
+ATOM    715  CE  MET A  97     -21.484  -7.324 -22.587  1.00 70.81           C  
+ANISOU  715  CE  MET A  97     9359   8848   8698    213   1836   -305       C  
+ATOM    716  N   LEU A  98     -26.060  -3.361 -25.977  1.00101.64           N  
+ANISOU  716  N   LEU A  98    12055  13191  13371    583   1974     95       N  
+ATOM    717  CA  LEU A  98     -27.090  -2.306 -25.727  1.00104.44           C  
+ANISOU  717  CA  LEU A  98    12260  13563  13858    803   2175    216       C  
+ATOM    718  C   LEU A  98     -27.843  -1.768 -26.965  1.00 99.32           C  
+ANISOU  718  C   LEU A  98    11253  13135  13349    890   2107    411       C  
+ATOM    719  O   LEU A  98     -27.308  -1.714 -28.071  1.00 91.78           O  
+ANISOU  719  O   LEU A  98    10232  12263  12378    839   1898    441       O  
+ATOM    720  CB  LEU A  98     -26.469  -1.140 -24.941  1.00 98.56           C  
+ANISOU  720  CB  LEU A  98    11797  12554  13097    977   2303    129       C  
+TER     721      LEU A  98                                                      
+ATOM    722  N   ALA B   2     -32.420 -24.500 -28.343  1.00 55.40           N  
+ANISOU  722  N   ALA B   2     8165   6777   6106   -670  -1057   -125       N  
+ATOM    723  CA  ALA B   2     -32.280 -23.018 -28.309  1.00 49.74           C  
+ANISOU  723  CA  ALA B   2     7221   6215   5463   -512   -965    -28       C  
+ATOM    724  C   ALA B   2     -30.968 -22.594 -27.656  1.00 49.10           C  
+ANISOU  724  C   ALA B   2     7123   6073   5460   -324   -756    -44       C  
+ATOM    725  O   ALA B   2     -30.475 -23.240 -26.699  1.00 48.76           O  
+ANISOU  725  O   ALA B   2     7101   5932   5490   -308   -687    -81       O  
+ATOM    726  CB  ALA B   2     -33.452 -22.398 -27.562  1.00 46.79           C  
+ANISOU  726  CB  ALA B   2     6548   6005   5225   -580  -1026     92       C  
+ATOM    727  N   THR B   3     -30.475 -21.450 -28.119  1.00 46.70           N  
+ANISOU  727  N   THR B   3     6765   5842   5136   -203   -668      1       N  
+ATOM    728  CA  THR B   3     -29.337 -20.783 -27.525  1.00 45.09           C  
+ANISOU  728  CA  THR B   3     6493   5632   5006    -79   -488      8       C  
+ATOM    729  C   THR B   3     -29.711 -19.332 -27.227  1.00 42.65           C  
+ANISOU  729  C   THR B   3     6022   5395   4786    -46   -461    119       C  
+ATOM    730  O   THR B   3     -30.163 -18.603 -28.102  1.00 49.78           O  
+ANISOU  730  O   THR B   3     6948   6349   5617    -31   -515    186       O  
+ATOM    731  CB  THR B   3     -28.152 -20.886 -28.525  1.00 48.51           C  
+ANISOU  731  CB  THR B   3     7083   6061   5285     14   -383    -53       C  
+ATOM    732  OG1 THR B   3     -27.960 -22.272 -28.848  1.00 53.59           O  
+ANISOU  732  OG1 THR B   3     7925   6609   5827     21   -421   -170       O  
+ATOM    733  CG2 THR B   3     -26.865 -20.283 -27.959  1.00 46.16           C  
+ANISOU  733  CG2 THR B   3     6683   5804   5049    105   -200    -45       C  
+ATOM    734  N   TYR B   4     -29.515 -18.935 -25.980  1.00 41.02           N  
+ANISOU  734  N   TYR B   4     5685   5178   4720    -22   -381    136       N  
+ATOM    735  CA  TYR B   4     -29.849 -17.616 -25.484  1.00 41.59           C  
+ANISOU  735  CA  TYR B   4     5649   5273   4878     26   -345    216       C  
+ATOM    736  C   TYR B   4     -28.595 -16.874 -25.182  1.00 37.08           C  
+ANISOU  736  C   TYR B   4     5099   4664   4323     55   -200    205       C  
+ATOM    737  O   TYR B   4     -27.552 -17.444 -25.084  1.00 42.67           O  
+ANISOU  737  O   TYR B   4     5829   5376   5007     49   -128    142       O  
+ATOM    738  CB  TYR B   4     -30.686 -17.729 -24.208  1.00 37.93           C  
+ANISOU  738  CB  TYR B   4     5032   4839   4538     12   -366    231       C  
+ATOM    739  CG  TYR B   4     -31.986 -18.470 -24.482  1.00 40.65           C  
+ANISOU  739  CG  TYR B   4     5310   5268   4864    -68   -514    257       C  
+ATOM    740  CD1 TYR B   4     -32.953 -17.916 -25.304  1.00 41.09           C  
+ANISOU  740  CD1 TYR B   4     5314   5421   4875    -38   -621    333       C  
+ATOM    741  CD2 TYR B   4     -32.253 -19.691 -23.893  1.00 39.18           C  
+ANISOU  741  CD2 TYR B   4     5113   5074   4699   -188   -554    219       C  
+ATOM    742  CE1 TYR B   4     -34.139 -18.580 -25.546  1.00 44.88           C  
+ANISOU  742  CE1 TYR B   4     5690   6029   5332   -146   -773    362       C  
+ATOM    743  CE2 TYR B   4     -33.429 -20.383 -24.132  1.00 44.73           C  
+ANISOU  743  CE2 TYR B   4     5750   5865   5377   -328   -695    249       C  
+ATOM    744  CZ  TYR B   4     -34.369 -19.827 -24.951  1.00 49.31           C  
+ANISOU  744  CZ  TYR B   4     6235   6582   5915   -317   -807    316       C  
+ATOM    745  OH  TYR B   4     -35.506 -20.526 -25.188  1.00 53.31           O  
+ANISOU  745  OH  TYR B   4     6643   7219   6390   -490   -962    347       O  
+ATOM    746  N   LYS B   5     -28.735 -15.589 -25.005  1.00 42.61           N  
+ANISOU  746  N   LYS B   5     5794   5333   5063     87   -164    270       N  
+ATOM    747  CA  LYS B   5     -27.647 -14.685 -24.656  1.00 46.72           C  
+ANISOU  747  CA  LYS B   5     6346   5805   5598     57    -42    270       C  
+ATOM    748  C   LYS B   5     -27.871 -14.311 -23.218  1.00 44.65           C  
+ANISOU  748  C   LYS B   5     6004   5508   5453     71    -18    246       C  
+ATOM    749  O   LYS B   5     -28.949 -13.910 -22.869  1.00 45.52           O  
+ANISOU  749  O   LYS B   5     6085   5600   5610    146    -64    281       O  
+ATOM    750  CB  LYS B   5     -27.735 -13.411 -25.451  1.00 51.37           C  
+ANISOU  750  CB  LYS B   5     7063   6323   6130     68    -27    364       C  
+ATOM    751  CG  LYS B   5     -27.674 -13.596 -26.941  1.00 58.63           C  
+ANISOU  751  CG  LYS B   5     8089   7285   6902     63    -56    410       C  
+ATOM    752  CD  LYS B   5     -26.289 -13.986 -27.387  1.00 70.28           C  
+ANISOU  752  CD  LYS B   5     9582   8829   8291    -17     60    365       C  
+ATOM    753  CE  LYS B   5     -26.281 -14.277 -28.899  1.00 79.59           C  
+ANISOU  753  CE  LYS B   5    10887  10066   9288     -6     42    396       C  
+ATOM    754  NZ  LYS B   5     -26.107 -13.052 -29.737  1.00 78.80           N  
+ANISOU  754  NZ  LYS B   5    10935   9919   9086    -50     88    523       N  
+ATOM    755  N   VAL B   6     -26.848 -14.482 -22.400  1.00 44.73           N  
+ANISOU  755  N   VAL B   6     5968   5536   5490     12     52    185       N  
+ATOM    756  CA  VAL B   6     -26.898 -14.160 -21.017  1.00 43.45           C  
+ANISOU  756  CA  VAL B   6     5755   5350   5403      9     75    149       C  
+ATOM    757  C   VAL B   6     -25.875 -13.071 -20.817  1.00 41.71           C  
+ANISOU  757  C   VAL B   6     5600   5078   5168    -88    150    141       C  
+ATOM    758  O   VAL B   6     -24.703 -13.264 -21.100  1.00 40.03           O  
+ANISOU  758  O   VAL B   6     5351   4944   4913   -178    196    125       O  
+ATOM    759  CB  VAL B   6     -26.496 -15.357 -20.132  1.00 43.61           C  
+ANISOU  759  CB  VAL B   6     5675   5449   5445      0     68     89       C  
+ATOM    760  CG1 VAL B   6     -26.579 -14.975 -18.662  1.00 45.36           C  
+ANISOU  760  CG1 VAL B   6     5860   5659   5714     -5     90     55       C  
+ATOM    761  CG2 VAL B   6     -27.382 -16.547 -20.422  1.00 42.80           C  
+ANISOU  761  CG2 VAL B   6     5551   5370   5340     37     -7     99       C  
+ATOM    762  N   LYS B   7     -26.334 -11.940 -20.314  1.00 40.23           N  
+ANISOU  762  N   LYS B   7     5512   4765   5007    -71    162    150       N  
+ATOM    763  CA  LYS B   7     -25.489 -10.806 -20.042  1.00 45.32           C  
+ANISOU  763  CA  LYS B   7     6277   5311   5631   -205    217    138       C  
+ATOM    764  C   LYS B   7     -25.268 -10.732 -18.545  1.00 45.32           C  
+ANISOU  764  C   LYS B   7     6243   5315   5660   -241    224     48       C  
+ATOM    765  O   LYS B   7     -26.230 -10.649 -17.762  1.00 42.09           O  
+ANISOU  765  O   LYS B   7     5848   4860   5282   -112    213     21       O  
+ATOM    766  CB  LYS B   7     -26.179  -9.567 -20.522  1.00 45.61           C  
+ANISOU  766  CB  LYS B   7     6527   5150   5652   -141    218    203       C  
+ATOM    767  CG  LYS B   7     -25.518  -8.255 -20.177  1.00 54.48           C  
+ANISOU  767  CG  LYS B   7     7863   6090   6747   -291    265    191       C  
+ATOM    768  CD  LYS B   7     -26.348  -7.148 -20.886  1.00 64.52           C  
+ANISOU  768  CD  LYS B   7     9392   7132   7990   -162    255    284       C  
+ATOM    769  CE  LYS B   7     -25.977  -5.744 -20.437  1.00 79.55           C  
+ANISOU  769  CE  LYS B   7    11603   8759   9861   -274    292    266       C  
+ATOM    770  NZ  LYS B   7     -26.138  -4.714 -21.507  1.00 86.71           N  
+ANISOU  770  NZ  LYS B   7    12802   9439  10702   -264    295    396       N  
+ATOM    771  N   PHE B   8     -24.001 -10.796 -18.153  1.00 44.26           N  
+ANISOU  771  N   PHE B   8     6044   5273   5500   -411    242      4       N  
+ATOM    772  CA  PHE B   8     -23.636 -10.739 -16.757  1.00 48.27           C  
+ANISOU  772  CA  PHE B   8     6521   5811   6006   -472    227    -80       C  
+ATOM    773  C   PHE B   8     -23.203  -9.366 -16.431  1.00 50.61           C  
+ANISOU  773  C   PHE B   8     7012   5952   6265   -641    245   -114       C  
+ATOM    774  O   PHE B   8     -22.332  -8.836 -17.115  1.00 51.85           O  
+ANISOU  774  O   PHE B   8     7205   6107   6388   -833    269    -77       O  
+ATOM    775  CB  PHE B   8     -22.495 -11.714 -16.458  1.00 46.54           C  
+ANISOU  775  CB  PHE B   8     6090   5823   5767   -542    208   -104       C  
+ATOM    776  CG  PHE B   8     -22.919 -13.133 -16.573  1.00 43.20           C  
+ANISOU  776  CG  PHE B   8     5543   5501   5370   -371    182    -85       C  
+ATOM    777  CD1 PHE B   8     -23.753 -13.684 -15.611  1.00 45.99           C  
+ANISOU  777  CD1 PHE B   8     5889   5839   5743   -264    152   -107       C  
+ATOM    778  CD2 PHE B   8     -22.561 -13.888 -17.670  1.00 43.53           C  
+ANISOU  778  CD2 PHE B   8     5511   5629   5397   -326    196    -45       C  
+ATOM    779  CE1 PHE B   8     -24.172 -15.008 -15.719  1.00 45.51           C  
+ANISOU  779  CE1 PHE B   8     5756   5836   5697   -151    123    -79       C  
+ATOM    780  CE2 PHE B   8     -22.977 -15.203 -17.786  1.00 47.96           C  
+ANISOU  780  CE2 PHE B   8     6024   6230   5968   -183    163    -39       C  
+ATOM    781  CZ  PHE B   8     -23.809 -15.751 -16.817  1.00 42.32           C  
+ANISOU  781  CZ  PHE B   8     5316   5479   5284   -113    120    -50       C  
+ATOM    782  N   ILE B   9     -23.818  -8.777 -15.407  1.00 50.12           N  
+ANISOU  782  N   ILE B   9     7095   5752   6194   -582    242   -186       N  
+ATOM    783  CA  ILE B   9     -23.293  -7.532 -14.841  1.00 52.49           C  
+ANISOU  783  CA  ILE B   9     7627   5881   6436   -773    243   -255       C  
+ATOM    784  C   ILE B   9     -22.569  -7.908 -13.581  1.00 53.51           C  
+ANISOU  784  C   ILE B   9     7645   6168   6518   -894    195   -352       C  
+ATOM    785  O   ILE B   9     -23.199  -8.276 -12.624  1.00 53.62           O  
+ANISOU  785  O   ILE B   9     7645   6206   6520   -744    190   -409       O  
+ATOM    786  CB  ILE B   9     -24.432  -6.583 -14.587  1.00 57.52           C  
+ANISOU  786  CB  ILE B   9     8544   6244   7065   -590    275   -283       C  
+ATOM    787  CG1 ILE B   9     -25.188  -6.426 -15.903  1.00 59.96           C  
+ANISOU  787  CG1 ILE B   9     8902   6461   7416   -426    296   -159       C  
+ATOM    788  CG2 ILE B   9     -23.932  -5.267 -13.966  1.00 60.99           C  
+ANISOU  788  CG2 ILE B   9     9309   6437   7425   -785    272   -375       C  
+ATOM    789  CD1 ILE B   9     -26.172  -5.282 -15.905  1.00 63.59           C  
+ANISOU  789  CD1 ILE B   9     9670   6630   7859   -227    324   -158       C  
+ATOM    790  N   THR B  10     -21.243  -7.928 -13.622  1.00 58.51           N  
+ANISOU  790  N   THR B  10     8157   6958   7116  -1157    160   -355       N  
+ATOM    791  CA  THR B  10     -20.440  -8.325 -12.483  1.00 58.08           C  
+ANISOU  791  CA  THR B  10     7958   7106   7001  -1275     86   -431       C  
+ATOM    792  C   THR B  10     -19.973  -7.044 -11.813  1.00 70.23           C  
+ANISOU  792  C   THR B  10     9748   8484   8451  -1550     48   -529       C  
+ATOM    793  O   THR B  10     -20.144  -5.958 -12.368  1.00 71.35           O  
+ANISOU  793  O   THR B  10    10161   8360   8588  -1655     87   -519       O  
+ATOM    794  CB  THR B  10     -19.189  -9.135 -12.876  1.00 58.06           C  
+ANISOU  794  CB  THR B  10     7627   7434   6998  -1387     54   -376       C  
+ATOM    795  OG1 THR B  10     -18.233  -8.281 -13.503  1.00 67.21           O  
+ANISOU  795  OG1 THR B  10     8801   8610   8125  -1697     67   -349       O  
+ATOM    796  CG2 THR B  10     -19.528 -10.276 -13.818  1.00 59.69           C  
+ANISOU  796  CG2 THR B  10     7661   7742   7275  -1147    101   -286       C  
+ATOM    797  N   PRO B  11     -19.376  -7.160 -10.620  1.00 72.85           N  
+ANISOU  797  N   PRO B  11    10022   8962   8697  -1676    -39   -622       N  
+ATOM    798  CA  PRO B  11     -18.837  -5.933 -10.022  1.00 82.51           C  
+ANISOU  798  CA  PRO B  11    11506  10030   9814  -1997    -96   -729       C  
+ATOM    799  C   PRO B  11     -17.740  -5.357 -10.913  1.00 82.13           C  
+ANISOU  799  C   PRO B  11    11402  10036   9765  -2359   -105   -662       C  
+ATOM    800  O   PRO B  11     -17.601  -4.166 -11.043  1.00 81.04           O  
+ANISOU  800  O   PRO B  11    11578   9634   9578  -2614   -104   -697       O  
+ATOM    801  CB  PRO B  11     -18.263  -6.417  -8.685  1.00 79.55           C  
+ANISOU  801  CB  PRO B  11    10990   9902   9333  -2070   -213   -819       C  
+ATOM    802  CG  PRO B  11     -19.024  -7.665  -8.373  1.00 77.41           C  
+ANISOU  802  CG  PRO B  11    10544   9762   9107  -1699   -182   -776       C  
+ATOM    803  CD  PRO B  11     -19.316  -8.308  -9.700  1.00 70.96           C  
+ANISOU  803  CD  PRO B  11     9555   8976   8429  -1526    -97   -639       C  
+ATOM    804  N   GLU B  12     -17.008  -6.230 -11.575  1.00 88.50           N  
+ANISOU  804  N   GLU B  12    11824  11180  10621  -2365    -98   -558       N  
+ATOM    805  CA  GLU B  12     -15.873  -5.804 -12.367  1.00 99.06           C  
+ANISOU  805  CA  GLU B  12    13027  12669  11940  -2715    -89   -484       C  
+ATOM    806  C   GLU B  12     -16.299  -5.351 -13.766  1.00 93.10           C  
+ANISOU  806  C   GLU B  12    12432  11697  11242  -2687     35   -371       C  
+ATOM    807  O   GLU B  12     -15.498  -4.776 -14.476  1.00 97.19           O  
+ANISOU  807  O   GLU B  12    12930  12268  11727  -3008     67   -299       O  
+ATOM    808  CB  GLU B  12     -14.832  -6.940 -12.446  1.00112.44           C  
+ANISOU  808  CB  GLU B  12    14216  14866  13638  -2694   -123   -425       C  
+ATOM    809  CG  GLU B  12     -14.678  -7.719 -11.130  1.00124.13           C  
+ANISOU  809  CG  GLU B  12    15529  16561  15070  -2562   -247   -503       C  
+ATOM    810  CD  GLU B  12     -13.339  -8.441 -10.973  1.00129.71           C  
+ANISOU  810  CD  GLU B  12    15773  17775  15735  -2649   -327   -459       C  
+ATOM    811  OE1 GLU B  12     -12.591  -8.120 -10.015  1.00122.40           O  
+ANISOU  811  OE1 GLU B  12    14767  17032  14705  -2906   -469   -526       O  
+ATOM    812  OE2 GLU B  12     -13.042  -9.343 -11.788  1.00121.66           O  
+ANISOU  812  OE2 GLU B  12    14470  16981  14772  -2441   -255   -362       O  
+ATOM    813  N   GLY B  13     -17.543  -5.608 -14.166  1.00 81.49           N  
+ANISOU  813  N   GLY B  13    11109  10009   9842  -2323     99   -344       N  
+ATOM    814  CA  GLY B  13     -18.037  -5.147 -15.451  1.00 73.28           C  
+ANISOU  814  CA  GLY B  13    10250   8758   8835  -2271    193   -234       C  
+ATOM    815  C   GLY B  13     -18.997  -6.122 -16.098  1.00 65.13           C  
+ANISOU  815  C   GLY B  13     9104   7761   7882  -1867    241   -172       C  
+ATOM    816  O   GLY B  13     -19.539  -6.995 -15.467  1.00 67.40           O  
+ANISOU  816  O   GLY B  13     9263   8138   8207  -1617    210   -222       O  
+ATOM    817  N   GLU B  14     -19.185  -5.957 -17.384  1.00 61.80           N  
+ANISOU  817  N   GLU B  14     8743   7270   7466  -1838    311    -57       N  
+ATOM    818  CA  GLU B  14     -20.256  -6.598 -18.125  1.00 63.32           C  
+ANISOU  818  CA  GLU B  14     8924   7423   7712  -1496    338      2       C  
+ATOM    819  C   GLU B  14     -19.671  -7.497 -19.189  1.00 56.31           C  
+ANISOU  819  C   GLU B  14     7774   6809   6810  -1480    388     83       C  
+ATOM    820  O   GLU B  14     -18.634  -7.194 -19.774  1.00 62.63           O  
+ANISOU  820  O   GLU B  14     8502   7742   7551  -1731    443    140       O  
+ATOM    821  CB  GLU B  14     -21.129  -5.544 -18.792  1.00 71.21           C  
+ANISOU  821  CB  GLU B  14    10284   8074   8699  -1428    362     71       C  
+ATOM    822  CG  GLU B  14     -22.416  -5.260 -18.043  1.00 86.78           C  
+ANISOU  822  CG  GLU B  14    12442   9819  10709  -1152    330      6       C  
+ATOM    823  CD  GLU B  14     -22.957  -3.842 -18.244  1.00101.03           C  
+ANISOU  823  CD  GLU B  14    14681  11229  12476  -1139    343     36       C  
+ATOM    824  OE1 GLU B  14     -22.373  -2.917 -17.631  1.00107.53           O  
+ANISOU  824  OE1 GLU B  14    15741  11869  13245  -1388    335    -29       O  
+ATOM    825  OE2 GLU B  14     -23.973  -3.658 -18.983  1.00100.60           O  
+ANISOU  825  OE2 GLU B  14    14745  11041  12435   -874    348    124       O  
+ATOM    826  N   LEU B  15     -20.365  -8.587 -19.454  1.00 56.17           N  
+ANISOU  826  N   LEU B  15     7631   6874   6835  -1191    377     86       N  
+ATOM    827  CA  LEU B  15     -20.023  -9.507 -20.528  1.00 55.27           C  
+ANISOU  827  CA  LEU B  15     7340   6967   6692  -1109    425    143       C  
+ATOM    828  C   LEU B  15     -21.290 -10.308 -20.860  1.00 53.66           C  
+ANISOU  828  C   LEU B  15     7166   6692   6529   -812    384    148       C  
+ATOM    829  O   LEU B  15     -22.039 -10.720 -19.940  1.00 50.69           O  
+ANISOU  829  O   LEU B  15     6774   6269   6216   -671    324     88       O  
+ATOM    830  CB  LEU B  15     -18.948 -10.454 -20.044  1.00 57.82           C  
+ANISOU  830  CB  LEU B  15     7356   7605   7007  -1128    426     93       C  
+ATOM    831  CG  LEU B  15     -18.440 -11.420 -21.099  1.00 63.30           C  
+ANISOU  831  CG  LEU B  15     7878   8524   7650  -1015    495    130       C  
+ATOM    832  CD1 LEU B  15     -17.756 -10.666 -22.216  1.00 63.58           C  
+ANISOU  832  CD1 LEU B  15     7943   8622   7594  -1222    602    221       C  
+ATOM    833  CD2 LEU B  15     -17.443 -12.372 -20.490  1.00 65.97           C  
+ANISOU  833  CD2 LEU B  15     7922   9161   7982   -958    487     79       C  
+ATOM    834  N   GLU B  16     -21.532 -10.510 -22.157  1.00 47.63           N  
+ANISOU  834  N   GLU B  16     6447   5937   5713   -745    415    221       N  
+ATOM    835  CA  GLU B  16     -22.664 -11.304 -22.654  1.00 45.67           C  
+ANISOU  835  CA  GLU B  16     6218   5656   5479   -515    358    230       C  
+ATOM    836  C   GLU B  16     -22.099 -12.584 -23.254  1.00 48.61           C  
+ANISOU  836  C   GLU B  16     6436   6232   5799   -443    384    205       C  
+ATOM    837  O   GLU B  16     -21.055 -12.553 -23.930  1.00 46.18           O  
+ANISOU  837  O   GLU B  16     6067   6070   5407   -536    474    229       O  
+ATOM    838  CB  GLU B  16     -23.451 -10.553 -23.698  1.00 48.11           C  
+ANISOU  838  CB  GLU B  16     6731   5809   5738   -476    346    328       C  
+ATOM    839  CG  GLU B  16     -24.832 -11.113 -24.032  1.00 53.37           C  
+ANISOU  839  CG  GLU B  16     7413   6439   6424   -265    251    343       C  
+ATOM    840  CD  GLU B  16     -25.747 -10.126 -24.829  1.00 57.72           C  
+ANISOU  840  CD  GLU B  16     8169   6829   6932   -188    209    453       C  
+ATOM    841  OE1 GLU B  16     -26.936  -9.937 -24.446  1.00 69.98           O  
+ANISOU  841  OE1 GLU B  16     9737   8308   8544    -25    134    464       O  
+ATOM    842  OE2 GLU B  16     -25.279  -9.506 -25.809  1.00 71.51           O  
+ANISOU  842  OE2 GLU B  16    10058   8536   8577   -278    255    541       O  
+ATOM    843  N   VAL B  17     -22.770 -13.706 -22.978  1.00 44.60           N  
+ANISOU  843  N   VAL B  17     5878   5736   5329   -281    315    156       N  
+ATOM    844  CA  VAL B  17     -22.304 -14.976 -23.436  1.00 46.75           C  
+ANISOU  844  CA  VAL B  17     6070   6143   5548   -182    330    114       C  
+ATOM    845  C   VAL B  17     -23.463 -15.746 -23.995  1.00 45.90           C  
+ANISOU  845  C   VAL B  17     6061   5952   5427    -66    243    110       C  
+ATOM    846  O   VAL B  17     -24.614 -15.485 -23.683  1.00 43.95           O  
+ANISOU  846  O   VAL B  17     5860   5598   5240    -49    164    134       O  
+ATOM    847  CB  VAL B  17     -21.605 -15.796 -22.302  1.00 47.60           C  
+ANISOU  847  CB  VAL B  17     6021   6360   5702   -132    323     46       C  
+ATOM    848  CG1 VAL B  17     -20.698 -14.897 -21.492  1.00 51.12           C  
+ANISOU  848  CG1 VAL B  17     6363   6888   6173   -288    361     47       C  
+ATOM    849  CG2 VAL B  17     -22.618 -16.422 -21.353  1.00 49.09           C  
+ANISOU  849  CG2 VAL B  17     6236   6442   5970    -53    227     18       C  
+ATOM    850  N   GLU B  18     -23.109 -16.745 -24.776  1.00 46.07           N  
+ANISOU  850  N   GLU B  18     6102   6043   5357     16    260     72       N  
+ATOM    851  CA  GLU B  18     -24.020 -17.745 -25.270  1.00 49.63           C  
+ANISOU  851  CA  GLU B  18     6660   6424   5772     95    165     41       C  
+ATOM    852  C   GLU B  18     -24.215 -18.851 -24.218  1.00 44.35           C  
+ANISOU  852  C   GLU B  18     5956   5714   5177    154    106    -15       C  
+ATOM    853  O   GLU B  18     -23.267 -19.284 -23.560  1.00 51.13           O  
+ANISOU  853  O   GLU B  18     6734   6641   6052    214    157    -53       O  
+ATOM    854  CB  GLU B  18     -23.469 -18.355 -26.555  1.00 50.78           C  
+ANISOU  854  CB  GLU B  18     6901   6634   5756    163    218      4       C  
+ATOM    855  CG  GLU B  18     -23.996 -17.686 -27.802  1.00 68.77           C  
+ANISOU  855  CG  GLU B  18     9305   8898   7926    113    200     68       C  
+ATOM    856  CD  GLU B  18     -23.835 -18.551 -29.075  1.00 88.05           C  
+ANISOU  856  CD  GLU B  18    11901  11375  10178    191    210      8       C  
+ATOM    857  OE1 GLU B  18     -22.896 -19.410 -29.126  1.00 81.31           O  
+ANISOU  857  OE1 GLU B  18    11040  10592   9262    305    301    -77       O  
+ATOM    858  OE2 GLU B  18     -24.664 -18.355 -30.020  1.00 95.29           O  
+ANISOU  858  OE2 GLU B  18    12955  12254  10995    158    122     45       O  
+ATOM    859  N   CYS B  19     -25.445 -19.302 -24.075  1.00 41.64           N  
+ANISOU  859  N   CYS B  19     5672   5279   4869    130     -6     -8       N  
+ATOM    860  CA  CYS B  19     -25.763 -20.344 -23.133  1.00 45.79           C  
+ANISOU  860  CA  CYS B  19     6202   5746   5449    144    -63    -39       C  
+ATOM    861  C   CYS B  19     -26.882 -21.159 -23.766  1.00 46.84           C  
+ANISOU  861  C   CYS B  19     6462   5798   5535     89   -183    -46       C  
+ATOM    862  O   CYS B  19     -27.984 -20.631 -23.986  1.00 45.31           O  
+ANISOU  862  O   CYS B  19     6227   5622   5365     10   -256      7       O  
+ATOM    863  CB  CYS B  19     -26.236 -19.742 -21.802  1.00 44.81           C  
+ANISOU  863  CB  CYS B  19     5955   5628   5442     93    -68      2       C  
+ATOM    864  SG  CYS B  19     -26.514 -21.029 -20.541  1.00 44.98           S  
+ANISOU  864  SG  CYS B  19     5996   5591   5503     93   -120     -8       S  
+ATOM    865  N   ASP B  20     -26.627 -22.429 -24.061  1.00 46.35           N  
+ANISOU  865  N   ASP B  20     6561   5651   5398    132   -213   -114       N  
+ATOM    866  CA  ASP B  20     -27.710 -23.303 -24.531  1.00 48.89           C  
+ANISOU  866  CA  ASP B  20     7032   5874   5668     19   -349   -130       C  
+ATOM    867  C   ASP B  20     -28.747 -23.474 -23.465  1.00 47.10           C  
+ANISOU  867  C   ASP B  20     6711   5635   5547   -116   -420    -68       C  
+ATOM    868  O   ASP B  20     -28.472 -23.214 -22.296  1.00 47.38           O  
+ANISOU  868  O   ASP B  20     6628   5699   5673    -83   -357    -35       O  
+ATOM    869  CB  ASP B  20     -27.195 -24.650 -25.016  1.00 49.61           C  
+ANISOU  869  CB  ASP B  20     7385   5821   5642     92   -366   -229       C  
+ATOM    870  CG  ASP B  20     -26.366 -24.538 -26.278  1.00 56.74           C  
+ANISOU  870  CG  ASP B  20     8391   6766   6398    224   -291   -299       C  
+ATOM    871  OD1 ASP B  20     -26.482 -23.537 -27.079  1.00 61.65           O  
+ANISOU  871  OD1 ASP B  20     8935   7508   6978    194   -270   -261       O  
+ATOM    872  OD2 ASP B  20     -25.587 -25.487 -26.498  1.00 64.45           O  
+ANISOU  872  OD2 ASP B  20     9551   7653   7283    379   -246   -389       O  
+ATOM    873  N   ASP B  21     -29.960 -23.866 -23.882  1.00 51.35           N  
+ANISOU  873  N   ASP B  21     7285   6165   6058   -283   -552    -48       N  
+ATOM    874  CA  ASP B  21     -31.093 -24.022 -22.958  1.00 47.36           C  
+ANISOU  874  CA  ASP B  21     6647   5708   5637   -444   -612     27       C  
+ATOM    875  C   ASP B  21     -30.985 -25.153 -21.926  1.00 47.41           C  
+ANISOU  875  C   ASP B  21     6767   5582   5664   -512   -610     28       C  
+ATOM    876  O   ASP B  21     -31.828 -25.247 -21.025  1.00 45.27           O  
+ANISOU  876  O   ASP B  21     6372   5373   5454   -650   -626    105       O  
+ATOM    877  CB  ASP B  21     -32.458 -24.057 -23.695  1.00 51.66           C  
+ANISOU  877  CB  ASP B  21     7134   6351   6143   -629   -764     67       C  
+ATOM    878  CG  ASP B  21     -32.657 -25.259 -24.632  1.00 61.29           C  
+ANISOU  878  CG  ASP B  21     8623   7436   7229   -779   -899     -7       C  
+ATOM    879  OD1 ASP B  21     -31.869 -26.233 -24.690  1.00 60.99           O  
+ANISOU  879  OD1 ASP B  21     8860   7188   7124   -738   -879    -93       O  
+ATOM    880  OD2 ASP B  21     -33.671 -25.198 -25.362  1.00 76.44           O  
+ANISOU  880  OD2 ASP B  21    10482   9466   9093   -935  -1042     19       O  
+ATOM    881  N   ASP B  22     -29.986 -26.019 -22.094  1.00 45.76           N  
+ANISOU  881  N   ASP B  22     6801   5197   5386   -402   -588    -47       N  
+ATOM    882  CA  ASP B  22     -29.698 -27.103 -21.184  1.00 49.94           C  
+ANISOU  882  CA  ASP B  22     7499   5560   5913   -408   -587    -39       C  
+ATOM    883  C   ASP B  22     -28.367 -26.870 -20.478  1.00 51.81           C  
+ANISOU  883  C   ASP B  22     7692   5815   6179   -156   -468    -51       C  
+ATOM    884  O   ASP B  22     -27.852 -27.770 -19.904  1.00 47.85           O  
+ANISOU  884  O   ASP B  22     7360   5171   5649    -76   -467    -52       O  
+ATOM    885  CB  ASP B  22     -29.681 -28.442 -21.915  1.00 54.09           C  
+ANISOU  885  CB  ASP B  22     8395   5838   6318   -461   -680   -116       C  
+ATOM    886  CG  ASP B  22     -28.657 -28.512 -23.084  1.00 63.91           C  
+ANISOU  886  CG  ASP B  22     9803   7027   7451   -230   -637   -239       C  
+ATOM    887  OD1 ASP B  22     -28.251 -27.429 -23.607  1.00 56.77           O  
+ANISOU  887  OD1 ASP B  22     8699   6311   6557   -118   -561   -247       O  
+ATOM    888  OD2 ASP B  22     -28.283 -29.685 -23.476  1.00 60.29           O  
+ANISOU  888  OD2 ASP B  22     9703   6324   6879   -163   -672   -325       O  
+ATOM    889  N   VAL B  23     -27.833 -25.644 -20.499  1.00 44.07           N  
+ANISOU  889  N   VAL B  23     6485   5013   5246    -45   -380    -50       N  
+ATOM    890  CA  VAL B  23     -26.611 -25.310 -19.757  1.00 47.28           C  
+ANISOU  890  CA  VAL B  23     6793   5491   5677    138   -286    -54       C  
+ATOM    891  C   VAL B  23     -26.941 -24.305 -18.663  1.00 46.19           C  
+ANISOU  891  C   VAL B  23     6430   5488   5630     71   -247      9       C  
+ATOM    892  O   VAL B  23     -27.644 -23.285 -18.881  1.00 39.27           O  
+ANISOU  892  O   VAL B  23     5415   4705   4798    -11   -238     32       O  
+ATOM    893  CB  VAL B  23     -25.523 -24.795 -20.707  1.00 50.38           C  
+ANISOU  893  CB  VAL B  23     7146   5975   6020    297   -208   -117       C  
+ATOM    894  CG1 VAL B  23     -24.342 -24.208 -19.967  1.00 46.76           C  
+ANISOU  894  CG1 VAL B  23     6507   5665   5593    423   -122   -109       C  
+ATOM    895  CG2 VAL B  23     -25.132 -25.955 -21.653  1.00 50.32           C  
+ANISOU  895  CG2 VAL B  23     7401   5823   5893    416   -228   -198       C  
+ATOM    896  N   TYR B  24     -26.524 -24.659 -17.451  1.00 44.23           N  
+ANISOU  896  N   TYR B  24     6178   5236   5390    119   -233     41       N  
+ATOM    897  CA  TYR B  24     -26.635 -23.726 -16.362  1.00 42.32           C  
+ANISOU  897  CA  TYR B  24     5758   5120   5199     83   -187     78       C  
+ATOM    898  C   TYR B  24     -25.823 -22.471 -16.675  1.00 41.44           C  
+ANISOU  898  C   TYR B  24     5501   5135   5109    147   -123     34       C  
+ATOM    899  O   TYR B  24     -24.735 -22.521 -17.198  1.00 44.52           O  
+ANISOU  899  O   TYR B  24     5887   5563   5465    255    -98     -5       O  
+ATOM    900  CB  TYR B  24     -26.178 -24.336 -15.052  1.00 44.23           C  
+ANISOU  900  CB  TYR B  24     6041   5350   5413    135   -194    117       C  
+ATOM    901  CG  TYR B  24     -27.087 -25.431 -14.497  1.00 46.96           C  
+ANISOU  901  CG  TYR B  24     6541   5568   5732     16   -244    192       C  
+ATOM    902  CD1 TYR B  24     -28.468 -25.241 -14.364  1.00 44.56           C  
+ANISOU  902  CD1 TYR B  24     6173   5299   5459   -181   -243    243       C  
+ATOM    903  CD2 TYR B  24     -26.538 -26.649 -14.079  1.00 51.68           C  
+ANISOU  903  CD2 TYR B  24     7347   6023   6266    106   -288    224       C  
+ATOM    904  CE1 TYR B  24     -29.285 -26.242 -13.871  1.00 49.24           C  
+ANISOU  904  CE1 TYR B  24     6889   5801   6017   -343   -281    325       C  
+ATOM    905  CE2 TYR B  24     -27.342 -27.663 -13.564  1.00 49.44           C  
+ANISOU  905  CE2 TYR B  24     7249   5591   5944    -40   -332    309       C  
+ATOM    906  CZ  TYR B  24     -28.691 -27.448 -13.430  1.00 51.30           C  
+ANISOU  906  CZ  TYR B  24     7400   5881   6209   -289   -324    362       C  
+ATOM    907  OH  TYR B  24     -29.429 -28.459 -12.887  1.00 52.12           O  
+ANISOU  907  OH  TYR B  24     7677   5862   6265   -476   -359    461       O  
+ATOM    908  N   VAL B  25     -26.397 -21.353 -16.303  1.00 42.58           N  
+ANISOU  908  N   VAL B  25     5534   5344   5298     74    -91     48       N  
+ATOM    909  CA  VAL B  25     -25.870 -19.977 -16.515  1.00 43.51           C  
+ANISOU  909  CA  VAL B  25     5561   5536   5435     77    -35     18       C  
+ATOM    910  C   VAL B  25     -24.479 -19.883 -15.914  1.00 45.47           C  
+ANISOU  910  C   VAL B  25     5750   5871   5655    125    -13    -11       C  
+ATOM    911  O   VAL B  25     -23.583 -19.234 -16.483  1.00 42.02           O  
+ANISOU  911  O   VAL B  25     5255   5505   5205    121     24    -37       O  
+ATOM    912  CB  VAL B  25     -27.014 -19.053 -15.974  1.00 47.07           C  
+ANISOU  912  CB  VAL B  25     5964   5993   5928     22    -14     42       C  
+ATOM    913  CG1 VAL B  25     -26.658 -17.985 -14.979  1.00 51.34           C  
+ANISOU  913  CG1 VAL B  25     6467   6569   6468     14     35     10       C  
+ATOM    914  CG2 VAL B  25     -27.951 -18.612 -17.124  1.00 50.07           C  
+ANISOU  914  CG2 VAL B  25     6347   6348   6328     11    -32     68       C  
+ATOM    915  N   LEU B  26     -24.262 -20.562 -14.781  1.00 42.91           N  
+ANISOU  915  N   LEU B  26     5432   5567   5305    159    -44      3       N  
+ATOM    916  CA  LEU B  26     -22.937 -20.508 -14.120  1.00 44.21           C  
+ANISOU  916  CA  LEU B  26     5508   5860   5427    214    -52    -16       C  
+ATOM    917  C   LEU B  26     -21.873 -21.156 -15.044  1.00 43.16           C  
+ANISOU  917  C   LEU B  26     5348   5786   5263    347    -46    -31       C  
+ATOM    918  O   LEU B  26     -20.782 -20.644 -15.204  1.00 41.77           O  
+ANISOU  918  O   LEU B  26     5032   5771   5066    355    -19    -54       O  
+ATOM    919  CB  LEU B  26     -22.973 -21.227 -12.757  1.00 43.87           C  
+ANISOU  919  CB  LEU B  26     5503   5824   5338    252   -103     21       C  
+ATOM    920  CG  LEU B  26     -21.633 -21.303 -12.009  1.00 51.12           C  
+ANISOU  920  CG  LEU B  26     6319   6909   6194    330   -147     15       C  
+ATOM    921  CD1 LEU B  26     -20.989 -19.928 -11.865  1.00 47.47           C  
+ANISOU  921  CD1 LEU B  26     5717   6587   5732    203   -127    -41       C  
+ATOM    922  CD2 LEU B  26     -21.802 -21.989 -10.650  1.00 53.81           C  
+ANISOU  922  CD2 LEU B  26     6734   7244   6465    368   -206     70       C  
+ATOM    923  N   ASP B  27     -22.221 -22.283 -15.633  1.00 44.33           N  
+ANISOU  923  N   ASP B  27     5638   5809   5394    443    -66    -21       N  
+ATOM    924  CA  ASP B  27     -21.332 -23.028 -16.510  1.00 46.01           C  
+ANISOU  924  CA  ASP B  27     5876   6049   5554    621    -47    -49       C  
+ATOM    925  C   ASP B  27     -20.956 -22.226 -17.766  1.00 49.22           C  
+ANISOU  925  C   ASP B  27     6200   6549   5953    583     32    -86       C  
+ATOM    926  O   ASP B  27     -19.802 -22.149 -18.106  1.00 50.44           O  
+ANISOU  926  O   ASP B  27     6223   6878   6063    680     86   -104       O  
+ATOM    927  CB  ASP B  27     -21.974 -24.337 -16.843  1.00 48.69           C  
+ANISOU  927  CB  ASP B  27     6461   6173   5864    695    -93    -45       C  
+ATOM    928  CG  ASP B  27     -22.021 -25.293 -15.605  1.00 61.91           C  
+ANISOU  928  CG  ASP B  27     8247   7761   7515    764   -163     12       C  
+ATOM    929  OD1 ASP B  27     -21.027 -25.395 -14.870  1.00 72.00           O  
+ANISOU  929  OD1 ASP B  27     9424   9171   8760    907   -177     30       O  
+ATOM    930  OD2 ASP B  27     -23.034 -25.974 -15.376  1.00 65.76           O  
+ANISOU  930  OD2 ASP B  27     8922   8059   8004    668   -211     51       O  
+ATOM    931  N   ALA B  28     -21.929 -21.573 -18.394  1.00 48.34           N  
+ANISOU  931  N   ALA B  28     6146   6346   5874    438     40    -82       N  
+ATOM    932  CA  ALA B  28     -21.708 -20.761 -19.556  1.00 48.04           C  
+ANISOU  932  CA  ALA B  28     6072   6368   5811    384    108    -93       C  
+ATOM    933  C   ALA B  28     -20.772 -19.641 -19.163  1.00 49.27           C  
+ANISOU  933  C   ALA B  28     6043   6698   5979    293    162    -84       C  
+ATOM    934  O   ALA B  28     -19.857 -19.319 -19.908  1.00 48.19           O  
+ANISOU  934  O   ALA B  28     5813   6707   5789    295    240    -88       O  
+ATOM    935  CB  ALA B  28     -23.039 -20.183 -20.056  1.00 52.12           C  
+ANISOU  935  CB  ALA B  28     6682   6758   6362    258     77    -68       C  
+ATOM    936  N   ALA B  29     -20.986 -19.058 -17.979  1.00 46.38           N  
+ANISOU  936  N   ALA B  29     5631   6327   5664    194    124    -74       N  
+ATOM    937  CA  ALA B  29     -20.076 -18.026 -17.489  1.00 48.20           C  
+ANISOU  937  CA  ALA B  29     5715   6706   5890     65    150    -79       C  
+ATOM    938  C   ALA B  29     -18.630 -18.516 -17.392  1.00 50.01           C  
+ANISOU  938  C   ALA B  29     5752   7184   6064    154    166    -86       C  
+ATOM    939  O   ALA B  29     -17.691 -17.860 -17.830  1.00 49.30           O  
+ANISOU  939  O   ALA B  29     5514   7276   5941     54    227    -80       O  
+ATOM    940  CB  ALA B  29     -20.518 -17.475 -16.122  1.00 48.24           C  
+ANISOU  940  CB  ALA B  29     5740   6659   5928    -29     96    -90       C  
+ATOM    941  N   GLU B  30     -18.455 -19.668 -16.787  1.00 50.74           N  
+ANISOU  941  N   GLU B  30     5842   7297   6140    344    111    -87       N  
+ATOM    942  CA  GLU B  30     -17.125 -20.211 -16.573  1.00 53.52           C  
+ANISOU  942  CA  GLU B  30     5996   7905   6434    495    109    -84       C  
+ATOM    943  C   GLU B  30     -16.487 -20.582 -17.882  1.00 55.58           C  
+ANISOU  943  C   GLU B  30     6200   8279   6639    634    213    -95       C  
+ATOM    944  O   GLU B  30     -15.310 -20.345 -18.062  1.00 53.30           O  
+ANISOU  944  O   GLU B  30     5662   8284   6302    650    267    -87       O  
+ATOM    945  CB  GLU B  30     -17.245 -21.433 -15.659  1.00 55.76           C  
+ANISOU  945  CB  GLU B  30     6364   8121   6701    708     18    -66       C  
+ATOM    946  CG  GLU B  30     -17.599 -20.966 -14.244  1.00 60.54           C  
+ANISOU  946  CG  GLU B  30     6973   8707   7322    564    -69    -52       C  
+ATOM    947  CD  GLU B  30     -17.847 -22.100 -13.266  1.00 67.44           C  
+ANISOU  947  CD  GLU B  30     7969   9491   8161    734   -157     -9       C  
+ATOM    948  OE1 GLU B  30     -18.209 -23.248 -13.665  1.00 66.53           O  
+ANISOU  948  OE1 GLU B  30     8035   9206   8037    915   -159      8       O  
+ATOM    949  OE2 GLU B  30     -17.669 -21.807 -12.069  1.00 71.86           O  
+ANISOU  949  OE2 GLU B  30     8471  10144   8689    666   -231      5       O  
+ATOM    950  N   GLU B  31     -17.279 -21.156 -18.796  1.00 55.65           N  
+ANISOU  950  N   GLU B  31     6432   8073   6637    723    241   -115       N  
+ATOM    951  CA  GLU B  31     -16.811 -21.477 -20.146  1.00 59.63           C  
+ANISOU  951  CA  GLU B  31     6942   8655   7058    853    350   -141       C  
+ATOM    952  C   GLU B  31     -16.291 -20.194 -20.865  1.00 55.72           C  
+ANISOU  952  C   GLU B  31     6283   8348   6540    632    457   -115       C  
+ATOM    953  O   GLU B  31     -15.355 -20.248 -21.599  1.00 58.65           O  
+ANISOU  953  O   GLU B  31     6505   8951   6826    714    569   -117       O  
+ATOM    954  CB  GLU B  31     -17.945 -22.145 -20.947  1.00 70.50           C  
+ANISOU  954  CB  GLU B  31     8629   9739   8417    905    329   -174       C  
+ATOM    955  CG  GLU B  31     -17.483 -23.157 -21.980  1.00 89.10           C  
+ANISOU  955  CG  GLU B  31    11093  12105  10654   1169    401   -233       C  
+ATOM    956  CD  GLU B  31     -16.540 -24.196 -21.373  1.00108.88           C  
+ANISOU  956  CD  GLU B  31    13534  14713  13120   1482    395   -248       C  
+ATOM    957  OE1 GLU B  31     -16.868 -24.715 -20.275  1.00122.63           O  
+ANISOU  957  OE1 GLU B  31    15352  16322  14918   1517    281   -221       O  
+ATOM    958  OE2 GLU B  31     -15.461 -24.475 -21.968  1.00106.25           O  
+ANISOU  958  OE2 GLU B  31    13067  14613  12689   1708    509   -276       O  
+ATOM    959  N   ALA B  32     -16.902 -19.037 -20.607  1.00 54.88           N  
+ANISOU  959  N   ALA B  32     6217   8134   6498    356    427    -85       N  
+ATOM    960  CA  ALA B  32     -16.492 -17.745 -21.179  1.00 59.73           C  
+ANISOU  960  CA  ALA B  32     6747   8857   7089    106    511    -44       C  
+ATOM    961  C   ALA B  32     -15.343 -17.016 -20.467  1.00 63.02           C  
+ANISOU  961  C   ALA B  32     6892   9546   7504    -75    520    -22       C  
+ATOM    962  O   ALA B  32     -14.998 -15.927 -20.905  1.00 63.67           O  
+ANISOU  962  O   ALA B  32     6934   9694   7561   -332    587     19       O  
+ATOM    963  CB  ALA B  32     -17.705 -16.806 -21.263  1.00 56.13           C  
+ANISOU  963  CB  ALA B  32     6511   8123   6691    -78    469    -20       C  
+ATOM    964  N   GLY B  33     -14.771 -17.574 -19.387  1.00 61.55           N  
+ANISOU  964  N   GLY B  33     6539   9514   7332     31    442    -42       N  
+ATOM    965  CA  GLY B  33     -13.600 -16.980 -18.707  1.00 63.73           C  
+ANISOU  965  CA  GLY B  33     6518  10110   7586   -146    423    -23       C  
+ATOM    966  C   GLY B  33     -13.895 -16.058 -17.525  1.00 66.50           C  
+ANISOU  966  C   GLY B  33     6927  10352   7985   -414    308    -38       C  
+ATOM    967  O   GLY B  33     -13.016 -15.338 -17.073  1.00 78.05           O  
+ANISOU  967  O   GLY B  33     8192  12044   9417   -656    282    -30       O  
+ATOM    968  N   ILE B  34     -15.129 -16.076 -17.028  1.00 67.68           N  
+ANISOU  968  N   ILE B  34     7348  10169   8195   -380    241    -66       N  
+ATOM    969  CA  ILE B  34     -15.538 -15.285 -15.866  1.00 69.74           C  
+ANISOU  969  CA  ILE B  34     7714  10302   8481   -573    147    -99       C  
+ATOM    970  C   ILE B  34     -15.518 -16.184 -14.636  1.00 64.98           C  
+ANISOU  970  C   ILE B  34     7061   9759   7866   -396     34   -118       C  
+ATOM    971  O   ILE B  34     -15.991 -17.333 -14.669  1.00 60.93           O  
+ANISOU  971  O   ILE B  34     6620   9161   7366   -127     24   -105       O  
+ATOM    972  CB  ILE B  34     -17.001 -14.806 -15.975  1.00 71.51           C  
+ANISOU  972  CB  ILE B  34     8249  10155   8763   -593    156   -112       C  
+ATOM    973  CG1 ILE B  34     -17.270 -14.074 -17.281  1.00 80.00           C  
+ANISOU  973  CG1 ILE B  34     9439  11114   9843   -696    254    -73       C  
+ATOM    974  CG2 ILE B  34     -17.370 -13.876 -14.827  1.00 74.50           C  
+ANISOU  974  CG2 ILE B  34     8756  10405   9144   -770     88   -161       C  
+ATOM    975  CD1 ILE B  34     -18.763 -13.913 -17.553  1.00 74.26           C  
+ANISOU  975  CD1 ILE B  34     8970  10076   9167   -610    251    -68       C  
+ATOM    976  N   ASP B  35     -15.021 -15.649 -13.537  1.00 61.68           N  
+ANISOU  976  N   ASP B  35     6562   9464   7408   -566    -59   -146       N  
+ATOM    977  CA  ASP B  35     -15.019 -16.414 -12.290  1.00 75.53           C  
+ANISOU  977  CA  ASP B  35     8296  11276   9122   -414   -177   -152       C  
+ATOM    978  C   ASP B  35     -16.098 -15.810 -11.437  1.00 67.96           C  
+ANISOU  978  C   ASP B  35     7599  10051   8171   -525   -210   -201       C  
+ATOM    979  O   ASP B  35     -16.004 -14.664 -11.028  1.00 71.36           O  
+ANISOU  979  O   ASP B  35     8091  10448   8572   -786   -232   -255       O  
+ATOM    980  CB  ASP B  35     -13.639 -16.434 -11.587  1.00 82.96           C  
+ANISOU  980  CB  ASP B  35     8931  12609   9978   -475   -282   -144       C  
+ATOM    981  CG  ASP B  35     -12.583 -17.205 -12.400  1.00 94.51           C  
+ANISOU  981  CG  ASP B  35    10096  14387  11425   -270   -232    -89       C  
+ATOM    982  OD1 ASP B  35     -12.806 -18.403 -12.759  1.00 96.53           O  
+ANISOU  982  OD1 ASP B  35    10403  14579  11694     79   -201    -57       O  
+ATOM    983  OD2 ASP B  35     -11.544 -16.586 -12.714  1.00 99.59           O  
+ANISOU  983  OD2 ASP B  35    10468  15337  12033   -469   -215    -78       O  
+ATOM    984  N   LEU B  36     -17.154 -16.583 -11.237  1.00 61.63           N  
+ANISOU  984  N   LEU B  36     6966   9051   7399   -328   -200   -183       N  
+ATOM    985  CA  LEU B  36     -18.261 -16.213 -10.383  1.00 56.78           C  
+ANISOU  985  CA  LEU B  36     6568   8229   6777   -371   -208   -218       C  
+ATOM    986  C   LEU B  36     -18.245 -17.129  -9.153  1.00 52.62           C  
+ANISOU  986  C   LEU B  36     6041   7780   6171   -238   -300   -192       C  
+ATOM    987  O   LEU B  36     -17.788 -18.261  -9.215  1.00 51.28           O  
+ANISOU  987  O   LEU B  36     5782   7714   5987    -45   -339   -130       O  
+ATOM    988  CB  LEU B  36     -19.602 -16.402 -11.121  1.00 60.32           C  
+ANISOU  988  CB  LEU B  36     7183   8425   7309   -276   -120   -195       C  
+ATOM    989  CG  LEU B  36     -19.852 -15.603 -12.408  1.00 57.54           C  
+ANISOU  989  CG  LEU B  36     6878   7960   7022   -360    -36   -197       C  
+ATOM    990  CD1 LEU B  36     -21.213 -16.023 -13.015  1.00 57.02           C  
+ANISOU  990  CD1 LEU B  36     6941   7702   7020   -235     11   -162       C  
+ATOM    991  CD2 LEU B  36     -19.778 -14.120 -12.106  1.00 59.01           C  
+ANISOU  991  CD2 LEU B  36     7159   8073   7187   -580    -26   -256       C  
+ATOM    992  N   PRO B  37     -18.782 -16.647  -8.045  1.00 49.77           N  
+ANISOU  992  N   PRO B  37     5814   7352   5742   -321   -326   -238       N  
+ATOM    993  CA  PRO B  37     -18.701 -17.404  -6.819  1.00 52.69           C  
+ANISOU  993  CA  PRO B  37     6200   7815   6003   -225   -415   -204       C  
+ATOM    994  C   PRO B  37     -19.633 -18.609  -6.877  1.00 53.75           C  
+ANISOU  994  C   PRO B  37     6445   7807   6169    -30   -373   -116       C  
+ATOM    995  O   PRO B  37     -20.659 -18.578  -7.575  1.00 52.82           O  
+ANISOU  995  O   PRO B  37     6420   7504   6142    -22   -275   -109       O  
+ATOM    996  CB  PRO B  37     -19.214 -16.410  -5.772  1.00 55.23           C  
+ANISOU  996  CB  PRO B  37     6682   8069   6232   -380   -415   -294       C  
+ATOM    997  CG  PRO B  37     -20.178 -15.544  -6.538  1.00 56.99           C  
+ANISOU  997  CG  PRO B  37     7035   8061   6556   -438   -287   -341       C  
+ATOM    998  CD  PRO B  37     -19.480 -15.359  -7.863  1.00 55.95           C  
+ANISOU  998  CD  PRO B  37     6768   7965   6526   -486   -269   -323       C  
+ATOM    999  N   TYR B  38     -19.264 -19.661  -6.164  1.00 51.10           N  
+ANISOU  999  N   TYR B  38     6105   7561   5748    112   -458    -39       N  
+ATOM   1000  CA  TYR B  38     -20.137 -20.809  -5.974  1.00 53.20           C  
+ANISOU 1000  CA  TYR B  38     6529   7673   6010    243   -434     55       C  
+ATOM   1001  C   TYR B  38     -19.656 -21.588  -4.747  1.00 54.18           C  
+ANISOU 1001  C   TYR B  38     6693   7909   5982    349   -548    134       C  
+ATOM   1002  O   TYR B  38     -18.582 -21.362  -4.322  1.00 49.82           O  
+ANISOU 1002  O   TYR B  38     6003   7570   5353    362   -654    116       O  
+ATOM   1003  CB  TYR B  38     -20.086 -21.734  -7.179  1.00 49.99           C  
+ANISOU 1003  CB  TYR B  38     6125   7167   5701    391   -407    104       C  
+ATOM   1004  CG  TYR B  38     -18.715 -22.275  -7.467  1.00 51.86           C  
+ANISOU 1004  CG  TYR B  38     6213   7579   5912    569   -486    127       C  
+ATOM   1005  CD1 TYR B  38     -17.850 -21.585  -8.312  1.00 55.55           C  
+ANISOU 1005  CD1 TYR B  38     6471   8204   6429    528   -464     64       C  
+ATOM   1006  CD2 TYR B  38     -18.269 -23.505  -6.904  1.00 61.75           C  
+ANISOU 1006  CD2 TYR B  38     7532   8850   7078    796   -577    225       C  
+ATOM   1007  CE1 TYR B  38     -16.594 -22.086  -8.614  1.00 58.14           C  
+ANISOU 1007  CE1 TYR B  38     6611   8752   6728    714   -515     89       C  
+ATOM   1008  CE2 TYR B  38     -16.989 -24.012  -7.186  1.00 59.46           C  
+ANISOU 1008  CE2 TYR B  38     7079   8753   6757   1025   -645    249       C  
+ATOM   1009  CZ  TYR B  38     -16.163 -23.294  -8.041  1.00 63.46           C  
+ANISOU 1009  CZ  TYR B  38     7329   9462   7319    985   -607    177       C  
+ATOM   1010  OH  TYR B  38     -14.891 -23.736  -8.343  1.00 72.30           O  
+ANISOU 1010  OH  TYR B  38     8229  10837   8402   1217   -652    201       O  
+ATOM   1011  N   SER B  39     -20.429 -22.569  -4.273  1.00 53.67           N  
+ANISOU 1011  N   SER B  39     6815   7706   5871    420   -534    237       N  
+ATOM   1012  CA  SER B  39     -19.980 -23.484  -3.243  1.00 53.24           C  
+ANISOU 1012  CA  SER B  39     6845   7718   5665    553   -645    347       C  
+ATOM   1013  C   SER B  39     -20.482 -24.911  -3.576  1.00 53.99           C  
+ANISOU 1013  C   SER B  39     7143   7585   5782    691   -631    477       C  
+ATOM   1014  O   SER B  39     -19.746 -25.715  -4.122  1.00 60.00           O  
+ANISOU 1014  O   SER B  39     7905   8323   6567    901   -692    520       O  
+ATOM   1015  CB  SER B  39     -20.438 -22.974  -1.880  1.00 54.47           C  
+ANISOU 1015  CB  SER B  39     7088   7945   5660    422   -647    339       C  
+ATOM   1016  OG  SER B  39     -19.961 -23.809  -0.856  1.00 58.10           O  
+ANISOU 1016  OG  SER B  39     7640   8485   5947    547   -768    457       O  
+ATOM   1017  N   CYS B  40     -21.745 -25.188  -3.303  1.00 53.52           N  
+ANISOU 1017  N   CYS B  40     7259   7360   5714    563   -542    532       N  
+ATOM   1018  CA  CYS B  40     -22.341 -26.502  -3.494  1.00 52.54           C  
+ANISOU 1018  CA  CYS B  40     7371   6999   5591    607   -533    661       C  
+ATOM   1019  C   CYS B  40     -22.554 -26.894  -4.990  1.00 54.29           C  
+ANISOU 1019  C   CYS B  40     7615   7039   5972    636   -494    621       C  
+ATOM   1020  O   CYS B  40     -22.599 -28.079  -5.354  1.00 56.18           O  
+ANISOU 1020  O   CYS B  40     8070   7067   6206    733   -528    702       O  
+ATOM   1021  CB  CYS B  40     -23.706 -26.493  -2.758  1.00 53.96           C  
+ANISOU 1021  CB  CYS B  40     7670   7122   5708    390   -431    727       C  
+ATOM   1022  SG  CYS B  40     -25.014 -25.506  -3.570  1.00 54.05           S  
+ANISOU 1022  SG  CYS B  40     7540   7122   5874    175   -270    621       S  
+ATOM   1023  N   ARG B  41     -22.745 -25.881  -5.830  1.00 55.21           N  
+ANISOU 1023  N   ARG B  41     7548   7218   6210    539   -423    498       N  
+ATOM   1024  CA  ARG B  41     -23.100 -26.036  -7.243  1.00 57.45           C  
+ANISOU 1024  CA  ARG B  41     7842   7361   6623    525   -377    449       C  
+ATOM   1025  C   ARG B  41     -24.289 -26.944  -7.426  1.00 53.39           C  
+ANISOU 1025  C   ARG B  41     7544   6624   6118    400   -351    531       C  
+ATOM   1026  O   ARG B  41     -24.325 -27.732  -8.363  1.00 57.10           O  
+ANISOU 1026  O   ARG B  41     8153   6914   6628    449   -373    531       O  
+ATOM   1027  CB  ARG B  41     -21.926 -26.568  -8.054  1.00 57.25           C  
+ANISOU 1027  CB  ARG B  41     7805   7331   6614    765   -433    421       C  
+ATOM   1028  CG  ARG B  41     -20.730 -25.656  -8.128  1.00 63.18           C  
+ANISOU 1028  CG  ARG B  41     8288   8346   7369    845   -452    341       C  
+ATOM   1029  CD  ARG B  41     -19.678 -26.364  -8.976  1.00 72.83           C  
+ANISOU 1029  CD  ARG B  41     9491   9584   8595   1112   -481    331       C  
+ATOM   1030  NE  ARG B  41     -20.005 -26.268 -10.416  1.00 66.24           N  
+ANISOU 1030  NE  ARG B  41     8672   8642   7853   1080   -399    256       N  
+ATOM   1031  CZ  ARG B  41     -19.501 -25.337 -11.206  1.00 60.12           C  
+ANISOU 1031  CZ  ARG B  41     7679   8033   7131   1040   -342    173       C  
+ATOM   1032  NH1 ARG B  41     -18.683 -24.440 -10.693  1.00 58.08           N  
+ANISOU 1032  NH1 ARG B  41     7175   8038   6852    995   -361    150       N  
+ATOM   1033  NH2 ARG B  41     -19.820 -25.271 -12.489  1.00 59.63           N  
+ANISOU 1033  NH2 ARG B  41     7655   7877   7124   1014   -273    118       N  
+ATOM   1034  N   ALA B  42     -25.254 -26.842  -6.528  1.00 50.75           N  
+ANISOU 1034  N   ALA B  42     7240   6313   5731    225   -301    598       N  
+ATOM   1035  CA  ALA B  42     -26.322 -27.854  -6.466  1.00 55.82           C  
+ANISOU 1035  CA  ALA B  42     8087   6773   6348     63   -286    714       C  
+ATOM   1036  C   ALA B  42     -27.689 -27.296  -6.092  1.00 53.85           C  
+ANISOU 1036  C   ALA B  42     7723   6630   6105   -178   -176    738       C  
+ATOM   1037  O   ALA B  42     -28.646 -28.060  -5.838  1.00 55.78           O  
+ANISOU 1037  O   ALA B  42     8091   6791   6308   -370   -150    854       O  
+ATOM   1038  CB  ALA B  42     -25.919 -28.950  -5.457  1.00 58.15           C  
+ANISOU 1038  CB  ALA B  42     8635   6960   6496    141   -354    856       C  
+ATOM   1039  N   GLY B  43     -27.766 -25.976  -6.007  1.00 52.94           N  
+ANISOU 1039  N   GLY B  43     7380   6706   6028   -168   -108    636       N  
+ATOM   1040  CA  GLY B  43     -29.019 -25.311  -5.704  1.00 57.58           C  
+ANISOU 1040  CA  GLY B  43     7828   7426   6621   -321      9    641       C  
+ATOM   1041  C   GLY B  43     -29.393 -25.157  -4.247  1.00 56.47           C  
+ANISOU 1041  C   GLY B  43     7699   7426   6330   -371     90    705       C  
+ATOM   1042  O   GLY B  43     -30.490 -24.676  -3.919  1.00 61.40           O  
+ANISOU 1042  O   GLY B  43     8200   8190   6936   -473    214    718       O  
+ATOM   1043  N   SER B  44     -28.507 -25.552  -3.359  1.00 57.15           N  
+ANISOU 1043  N   SER B  44     7922   7502   6288   -282     25    748       N  
+ATOM   1044  CA  SER B  44     -28.864 -25.573  -1.947  1.00 60.58           C  
+ANISOU 1044  CA  SER B  44     8415   8061   6539   -340     95    828       C  
+ATOM   1045  C   SER B  44     -28.070 -24.590  -1.083  1.00 55.02           C  
+ANISOU 1045  C   SER B  44     7667   7512   5724   -218     81    721       C  
+ATOM   1046  O   SER B  44     -27.939 -24.770   0.117  1.00 56.43           O  
+ANISOU 1046  O   SER B  44     7952   7776   5712   -219     84    785       O  
+ATOM   1047  CB  SER B  44     -28.724 -26.997  -1.455  1.00 64.11           C  
+ANISOU 1047  CB  SER B  44     9118   8363   6875   -384     27   1009       C  
+ATOM   1048  OG  SER B  44     -27.369 -27.403  -1.576  1.00 72.90           O  
+ANISOU 1048  OG  SER B  44    10341   9378   7978   -177   -128    997       O  
+ATOM   1049  N   CYS B  45     -27.538 -23.526  -1.680  1.00 50.30           N  
+ANISOU 1049  N   CYS B  45     6932   6949   5228   -137     60    559       N  
+ATOM   1050  CA  CYS B  45     -26.911 -22.490  -0.877  1.00 49.85           C  
+ANISOU 1050  CA  CYS B  45     6852   7028   5060    -85     47    441       C  
+ATOM   1051  C   CYS B  45     -27.172 -21.136  -1.520  1.00 51.33           C  
+ANISOU 1051  C   CYS B  45     6911   7228   5361    -83    119    279       C  
+ATOM   1052  O   CYS B  45     -27.967 -21.005  -2.440  1.00 55.12           O  
+ANISOU 1052  O   CYS B  45     7307   7650   5984   -106    191    278       O  
+ATOM   1053  CB  CYS B  45     -25.390 -22.791  -0.653  1.00 48.86           C  
+ANISOU 1053  CB  CYS B  45     6762   6928   4874     20   -134    439       C  
+ATOM   1054  SG  CYS B  45     -24.160 -22.368  -1.931  1.00 53.35           S  
+ANISOU 1054  SG  CYS B  45     7176   7476   5616    105   -244    330       S  
+ATOM   1055  N   SER B  46     -26.488 -20.125  -1.034  1.00 50.33           N  
+ANISOU 1055  N   SER B  46     6793   7170   5158    -63     86    148       N  
+ATOM   1056  CA  SER B  46     -26.687 -18.804  -1.525  1.00 53.49           C  
+ANISOU 1056  CA  SER B  46     7146   7540   5638    -62    151      0       C  
+ATOM   1057  C   SER B  46     -25.436 -18.250  -2.234  1.00 51.56           C  
+ANISOU 1057  C   SER B  46     6851   7262   5478    -77     28    -89       C  
+ATOM   1058  O   SER B  46     -25.397 -17.049  -2.580  1.00 51.57           O  
+ANISOU 1058  O   SER B  46     6861   7210   5522   -105     60   -215       O  
+ATOM   1059  CB  SER B  46     -27.077 -17.908  -0.321  1.00 54.94           C  
+ANISOU 1059  CB  SER B  46     7434   7804   5634    -60    242   -100       C  
+ATOM   1060  OG  SER B  46     -25.958 -17.693   0.515  1.00 59.45           O  
+ANISOU 1060  OG  SER B  46     8091   8449   6049    -97    114   -164       O  
+ATOM   1061  N   SER B  47     -24.417 -19.082  -2.465  1.00 50.22           N  
+ANISOU 1061  N   SER B  47     6631   7124   5322    -52   -104    -22       N  
+ATOM   1062  CA  SER B  47     -23.104 -18.545  -2.910  1.00 53.80           C  
+ANISOU 1062  CA  SER B  47     6993   7634   5811    -82   -216   -100       C  
+ATOM   1063  C   SER B  47     -23.102 -17.974  -4.299  1.00 49.57           C  
+ANISOU 1063  C   SER B  47     6378   7002   5454   -106   -173   -147       C  
+ATOM   1064  O   SER B  47     -22.409 -17.004  -4.556  1.00 47.90           O  
+ANISOU 1064  O   SER B  47     6131   6812   5254   -198   -204   -242       O  
+ATOM   1065  CB  SER B  47     -21.985 -19.587  -2.863  1.00 55.00           C  
+ANISOU 1065  CB  SER B  47     7072   7893   5931      4   -358    -10       C  
+ATOM   1066  OG  SER B  47     -21.799 -19.986  -1.539  1.00 67.17           O  
+ANISOU 1066  OG  SER B  47     8697   9542   7281     24   -428     35       O  
+ATOM   1067  N   CYS B  48     -23.836 -18.597  -5.210  1.00 47.83           N  
+ANISOU 1067  N   CYS B  48     6142   6677   5355    -48   -112    -75       N  
+ATOM   1068  CA  CYS B  48     -23.825 -18.180  -6.626  1.00 44.63           C  
+ANISOU 1068  CA  CYS B  48     5671   6187   5098    -57    -82   -102       C  
+ATOM   1069  C   CYS B  48     -25.021 -17.249  -6.959  1.00 50.82           C  
+ANISOU 1069  C   CYS B  48     6502   6866   5939    -77     30   -146       C  
+ATOM   1070  O   CYS B  48     -25.428 -17.128  -8.127  1.00 51.63           O  
+ANISOU 1070  O   CYS B  48     6573   6888   6154    -61     61   -130       O  
+ATOM   1071  CB  CYS B  48     -23.944 -19.426  -7.480  1.00 41.68           C  
+ANISOU 1071  CB  CYS B  48     5279   5758   4800     24   -100     -7       C  
+ATOM   1072  SG  CYS B  48     -25.514 -20.250  -7.174  1.00 47.58           S  
+ANISOU 1072  SG  CYS B  48     6110   6423   5543     17    -32     87       S  
+ATOM   1073  N   ALA B  49     -25.604 -16.621  -5.943  1.00 49.42           N  
+ANISOU 1073  N   ALA B  49     6406   6702   5668    -83     90   -197       N  
+ATOM   1074  CA  ALA B  49     -26.803 -15.852  -6.145  1.00 47.37           C  
+ANISOU 1074  CA  ALA B  49     6180   6371   5446    -34    205   -227       C  
+ATOM   1075  C   ALA B  49     -26.501 -14.656  -7.025  1.00 46.14           C  
+ANISOU 1075  C   ALA B  49     6068   6096   5364    -55    208   -304       C  
+ATOM   1076  O   ALA B  49     -25.486 -13.952  -6.837  1.00 47.19           O  
+ANISOU 1076  O   ALA B  49     6266   6210   5452   -154    153   -386       O  
+ATOM   1077  CB  ALA B  49     -27.369 -15.388  -4.811  1.00 48.90           C  
+ANISOU 1077  CB  ALA B  49     6469   6616   5493     -1    286   -284       C  
+ATOM   1078  N   GLY B  50     -27.414 -14.412  -7.959  1.00 46.35           N  
+ANISOU 1078  N   GLY B  50     6066   6052   5491     20    266   -269       N  
+ATOM   1079  CA  GLY B  50     -27.486 -13.112  -8.644  1.00 47.72           C  
+ANISOU 1079  CA  GLY B  50     6340   6080   5709     42    296   -328       C  
+ATOM   1080  C   GLY B  50     -28.933 -12.665  -8.683  1.00 52.51           C  
+ANISOU 1080  C   GLY B  50     6951   6666   6333    212    397   -314       C  
+ATOM   1081  O   GLY B  50     -29.796 -13.183  -7.949  1.00 51.98           O  
+ANISOU 1081  O   GLY B  50     6805   6723   6220    284    461   -282       O  
+ATOM   1082  N   LYS B  51     -29.194 -11.690  -9.542  1.00 56.73           N  
+ANISOU 1082  N   LYS B  51     7570   7061   6924    284    413   -325       N  
+ATOM   1083  CA  LYS B  51     -30.512 -11.104  -9.670  1.00 58.00           C  
+ANISOU 1083  CA  LYS B  51     7730   7209   7099    498    500   -309       C  
+ATOM   1084  C   LYS B  51     -30.801 -10.888 -11.160  1.00 51.95           C  
+ANISOU 1084  C   LYS B  51     6929   6374   6435    547    454   -226       C  
+ATOM   1085  O   LYS B  51     -30.004 -10.302 -11.879  1.00 52.34           O  
+ANISOU 1085  O   LYS B  51     7113   6268   6503    462    408   -238       O  
+ATOM   1086  CB  LYS B  51     -30.496  -9.813  -8.890  1.00 62.10           C  
+ANISOU 1086  CB  LYS B  51     8498   7573   7524    591    570   -437       C  
+ATOM   1087  CG  LYS B  51     -31.824  -9.123  -8.706  1.00 71.92           C  
+ANISOU 1087  CG  LYS B  51     9764   8816   8744    885    686   -447       C  
+ATOM   1088  CD  LYS B  51     -31.618  -8.015  -7.667  1.00 84.43           C  
+ANISOU 1088  CD  LYS B  51    11656  10230  10191    959    758   -609       C  
+ATOM   1089  CE  LYS B  51     -32.841  -7.727  -6.792  1.00 94.36           C  
+ANISOU 1089  CE  LYS B  51    12897  11600  11354   1256    917   -653       C  
+ATOM   1090  NZ  LYS B  51     -33.550  -6.484  -7.218  1.00 96.90           N  
+ANISOU 1090  NZ  LYS B  51    13408  11730  11677   1566    985   -687       N  
+ATOM   1091  N   VAL B  52     -31.914 -11.423 -11.620  1.00 50.92           N  
+ANISOU 1091  N   VAL B  52     6608   6386   6353    653    460   -133       N  
+ATOM   1092  CA  VAL B  52     -32.367 -11.250 -12.978  1.00 51.68           C  
+ANISOU 1092  CA  VAL B  52     6658   6458   6518    721    403    -47       C  
+ATOM   1093  C   VAL B  52     -32.869  -9.817 -13.125  1.00 55.73           C  
+ANISOU 1093  C   VAL B  52     7340   6819   7014    951    455    -71       C  
+ATOM   1094  O   VAL B  52     -33.750  -9.385 -12.411  1.00 58.68           O  
+ANISOU 1094  O   VAL B  52     7692   7253   7351   1160    545    -97       O  
+ATOM   1095  CB  VAL B  52     -33.490 -12.237 -13.328  1.00 54.96           C  
+ANISOU 1095  CB  VAL B  52     6806   7103   6972    744    375     55       C  
+ATOM   1096  CG1 VAL B  52     -34.003 -12.011 -14.775  1.00 52.68           C  
+ANISOU 1096  CG1 VAL B  52     6472   6811   6730    819    290    142       C  
+ATOM   1097  CG2 VAL B  52     -33.016 -13.669 -13.135  1.00 50.23           C  
+ANISOU 1097  CG2 VAL B  52     6115   6592   6375    524    325     77       C  
+ATOM   1098  N   VAL B  53     -32.237  -9.071 -14.009  1.00 58.89           N  
+ANISOU 1098  N   VAL B  53     7936   7012   7426    915    408    -62       N  
+ATOM   1099  CA  VAL B  53     -32.688  -7.736 -14.395  1.00 62.70           C  
+ANISOU 1099  CA  VAL B  53     8634   7295   7891   1137    434    -54       C  
+ATOM   1100  C   VAL B  53     -33.762  -7.758 -15.502  1.00 61.16           C  
+ANISOU 1100  C   VAL B  53     8295   7206   7737   1336    378     79       C  
+ATOM   1101  O   VAL B  53     -34.656  -6.932 -15.513  1.00 69.08           O  
+ANISOU 1101  O   VAL B  53     9355   8170   8723   1636    413    102       O  
+ATOM   1102  CB  VAL B  53     -31.492  -6.995 -14.961  1.00 67.39           C  
+ANISOU 1102  CB  VAL B  53     9512   7623   8467    954    398    -72       C  
+ATOM   1103  CG1 VAL B  53     -31.901  -5.593 -15.416  1.00 75.74           C  
+ANISOU 1103  CG1 VAL B  53    10871   8410   9495   1168    416    -46       C  
+ATOM   1104  CG2 VAL B  53     -30.375  -6.982 -13.920  1.00 67.44           C  
+ANISOU 1104  CG2 VAL B  53     9626   7572   8426    722    423   -198       C  
+ATOM   1105  N   SER B  54     -33.617  -8.645 -16.484  1.00 54.51           N  
+ANISOU 1105  N   SER B  54     7294   6485   6931   1182    280    163       N  
+ATOM   1106  CA  SER B  54     -34.604  -8.785 -17.528  1.00 57.42           C  
+ANISOU 1106  CA  SER B  54     7508   6990   7316   1325    196    285       C  
+ATOM   1107  C   SER B  54     -34.480 -10.128 -18.163  1.00 49.00           C  
+ANISOU 1107  C   SER B  54     6241   6104   6271   1103    103    329       C  
+ATOM   1108  O   SER B  54     -33.420 -10.732 -18.126  1.00 48.61           O  
+ANISOU 1108  O   SER B  54     6245   6001   6221    872    101    279       O  
+ATOM   1109  CB  SER B  54     -34.457  -7.676 -18.615  1.00 67.92           C  
+ANISOU 1109  CB  SER B  54     9097   8093   8615   1441    149    357       C  
+ATOM   1110  OG  SER B  54     -33.212  -7.732 -19.310  1.00 68.84           O  
+ANISOU 1110  OG  SER B  54     9383   8061   8712   1181    119    358       O  
+ATOM   1111  N   GLY B  55     -35.568 -10.582 -18.760  1.00 49.29           N  
+ANISOU 1111  N   GLY B  55     6054   6357   6315   1182     19    420       N  
+ATOM   1112  CA  GLY B  55     -35.709 -11.925 -19.288  1.00 50.10           C  
+ANISOU 1112  CA  GLY B  55     5974   6638   6423    971    -80    453       C  
+ATOM   1113  C   GLY B  55     -36.015 -12.954 -18.190  1.00 54.88           C  
+ANISOU 1113  C   GLY B  55     6384   7412   7052    843    -31    418       C  
+ATOM   1114  O   GLY B  55     -36.357 -12.606 -17.055  1.00 51.85           O  
+ANISOU 1114  O   GLY B  55     5948   7078   6673    954     81    384       O  
+ATOM   1115  N   SER B  56     -35.910 -14.235 -18.540  1.00 52.05           N  
+ANISOU 1115  N   SER B  56     5952   7132   6691    610   -114    429       N  
+ATOM   1116  CA  SER B  56     -36.309 -15.287 -17.628  1.00 53.81           C  
+ANISOU 1116  CA  SER B  56     6017   7504   6924    461    -86    428       C  
+ATOM   1117  C   SER B  56     -35.313 -16.444 -17.548  1.00 48.18           C  
+ANISOU 1117  C   SER B  56     5432   6672   6199    230   -112    379       C  
+ATOM   1118  O   SER B  56     -34.496 -16.695 -18.438  1.00 51.01           O  
+ANISOU 1118  O   SER B  56     5943   6898   6540    166   -175    352       O  
+ATOM   1119  CB  SER B  56     -37.721 -15.783 -17.988  1.00 54.48           C  
+ANISOU 1119  CB  SER B  56     5818   7872   7006    422   -173    525       C  
+ATOM   1120  OG  SER B  56     -37.776 -16.208 -19.330  1.00 61.00           O  
+ANISOU 1120  OG  SER B  56     6673   8698   7805    316   -335    559       O  
+ATOM   1121  N   VAL B  57     -35.377 -17.125 -16.430  1.00 52.89           N  
+ANISOU 1121  N   VAL B  57     5977   7324   6794    133    -50    372       N  
+ATOM   1122  CA  VAL B  57     -34.589 -18.335 -16.192  1.00 52.55           C  
+ANISOU 1122  CA  VAL B  57     6056   7179   6732    -51    -77    346       C  
+ATOM   1123  C   VAL B  57     -35.550 -19.389 -15.674  1.00 55.14           C  
+ANISOU 1123  C   VAL B  57     6247   7658   7045   -229    -95    418       C  
+ATOM   1124  O   VAL B  57     -36.603 -19.052 -15.133  1.00 53.51           O  
+ANISOU 1124  O   VAL B  57     5830   7660   6841   -192    -35    473       O  
+ATOM   1125  CB  VAL B  57     -33.487 -18.134 -15.162  1.00 52.68           C  
+ANISOU 1125  CB  VAL B  57     6199   7082   6734     -9     13    278       C  
+ATOM   1126  CG1 VAL B  57     -32.429 -17.171 -15.703  1.00 51.20           C  
+ANISOU 1126  CG1 VAL B  57     6147   6751   6553     92     24    213       C  
+ATOM   1127  CG2 VAL B  57     -34.091 -17.723 -13.810  1.00 53.07           C  
+ANISOU 1127  CG2 VAL B  57     6147   7252   6763     53    130    286       C  
+ATOM   1128  N   ASP B  58     -35.198 -20.651 -15.913  1.00 54.40           N  
+ANISOU 1128  N   ASP B  58     6283   7459   6926   -420   -174    422       N  
+ATOM   1129  CA  ASP B  58     -35.847 -21.810 -15.319  1.00 52.99           C  
+ANISOU 1129  CA  ASP B  58     6069   7345   6718   -650   -190    493       C  
+ATOM   1130  C   ASP B  58     -34.894 -22.245 -14.184  1.00 50.66           C  
+ANISOU 1130  C   ASP B  58     5942   6913   6390   -637   -113    472       C  
+ATOM   1131  O   ASP B  58     -33.754 -22.666 -14.424  1.00 47.29           O  
+ANISOU 1131  O   ASP B  58     5729   6287   5951   -598   -150    415       O  
+ATOM   1132  CB  ASP B  58     -36.003 -22.916 -16.375  1.00 56.52           C  
+ANISOU 1132  CB  ASP B  58     6638   7699   7137   -861   -345    501       C  
+ATOM   1133  CG  ASP B  58     -36.384 -24.259 -15.771  1.00 65.37           C  
+ANISOU 1133  CG  ASP B  58     7842   8781   8214  -1139   -373    568       C  
+ATOM   1134  OD1 ASP B  58     -36.846 -24.290 -14.603  1.00 66.65           O  
+ANISOU 1134  OD1 ASP B  58     7883   9073   8365  -1194   -270    640       O  
+ATOM   1135  OD2 ASP B  58     -36.259 -25.280 -16.483  1.00 70.20           O  
+ANISOU 1135  OD2 ASP B  58     8664   9224   8785  -1310   -494    551       O  
+ATOM   1136  N   GLN B  59     -35.324 -22.089 -12.942  1.00 54.05           N  
+ANISOU 1136  N   GLN B  59     6267   7475   6792   -640     -1    517       N  
+ATOM   1137  CA  GLN B  59     -34.515 -22.555 -11.829  1.00 56.53           C  
+ANISOU 1137  CA  GLN B  59     6742   7686   7049   -640     51    516       C  
+ATOM   1138  C   GLN B  59     -35.268 -23.486 -10.889  1.00 59.14           C  
+ANISOU 1138  C   GLN B  59     7050   8107   7313   -851     94    632       C  
+ATOM   1139  O   GLN B  59     -35.188 -23.390  -9.661  1.00 65.41           O  
+ANISOU 1139  O   GLN B  59     7848   8966   8035   -822    198    658       O  
+ATOM   1140  CB  GLN B  59     -33.848 -21.372 -11.086  1.00 52.52           C  
+ANISOU 1140  CB  GLN B  59     6227   7196   6529   -422    151    436       C  
+ATOM   1141  CG  GLN B  59     -34.803 -20.396 -10.480  1.00 52.17           C  
+ANISOU 1141  CG  GLN B  59     5988   7361   6471   -326    274    442       C  
+ATOM   1142  CD  GLN B  59     -34.109 -19.292  -9.719  1.00 53.41           C  
+ANISOU 1142  CD  GLN B  59     6218   7483   6592   -139    359    343       C  
+ATOM   1143  OE1 GLN B  59     -33.067 -19.483  -9.016  1.00 53.43           O  
+ANISOU 1143  OE1 GLN B  59     6375   7387   6535   -140    352    304       O  
+ATOM   1144  NE2 GLN B  59     -34.697 -18.133  -9.795  1.00 52.42           N  
+ANISOU 1144  NE2 GLN B  59     5992   7441   6483     26    432    304       N  
+ATOM   1145  N   SER B  60     -35.956 -24.435 -11.476  1.00 61.58           N  
+ANISOU 1145  N   SER B  60     7365   8407   7623  -1092      6    703       N  
+ATOM   1146  CA  SER B  60     -36.740 -25.363 -10.706  1.00 72.30           C  
+ANISOU 1146  CA  SER B  60     8709   9847   8911  -1360     39    834       C  
+ATOM   1147  C   SER B  60     -35.825 -26.402 -10.017  1.00 74.05           C  
+ANISOU 1147  C   SER B  60     9269   9808   9057  -1412     17    868       C  
+ATOM   1148  O   SER B  60     -36.221 -27.047  -9.059  1.00 79.84           O  
+ANISOU 1148  O   SER B  60    10049  10581   9705  -1588     76    985       O  
+ATOM   1149  CB  SER B  60     -37.836 -25.999 -11.579  1.00 70.49           C  
+ANISOU 1149  CB  SER B  60     8372   9709   8700  -1655    -64    902       C  
+ATOM   1150  OG  SER B  60     -37.380 -26.382 -12.862  1.00 66.63           O  
+ANISOU 1150  OG  SER B  60     8069   9001   8245  -1672   -224    825       O  
+ATOM   1151  N   ASP B  61     -34.586 -26.497 -10.469  1.00 73.32           N  
+ANISOU 1151  N   ASP B  61     9398   9476   8984  -1231    -57    775       N  
+ATOM   1152  CA  ASP B  61     -33.572 -27.336  -9.811  1.00 80.97           C  
+ANISOU 1152  CA  ASP B  61    10666  10220   9879  -1177    -83    802       C  
+ATOM   1153  C   ASP B  61     -32.954 -26.686  -8.541  1.00 78.11           C  
+ANISOU 1153  C   ASP B  61    10262   9960   9455   -993     15    795       C  
+ATOM   1154  O   ASP B  61     -32.067 -27.263  -7.927  1.00 77.14           O  
+ANISOU 1154  O   ASP B  61    10352   9697   9259   -910    -16    823       O  
+ATOM   1155  CB  ASP B  61     -32.442 -27.683 -10.824  1.00 80.12           C  
+ANISOU 1155  CB  ASP B  61    10771   9865   9803  -1012   -194    700       C  
+ATOM   1156  CG  ASP B  61     -32.957 -28.443 -12.071  1.00 80.27           C  
+ANISOU 1156  CG  ASP B  61    10914   9741   9842  -1194   -306    687       C  
+ATOM   1157  OD1 ASP B  61     -34.142 -28.856 -12.081  1.00 92.44           O  
+ANISOU 1157  OD1 ASP B  61    12396  11355  11371  -1491   -323    772       O  
+ATOM   1158  OD2 ASP B  61     -32.182 -28.623 -13.047  1.00 76.90           O  
+ANISOU 1158  OD2 ASP B  61    10638   9149   9429  -1052   -377    588       O  
+ATOM   1159  N   GLN B  62     -33.390 -25.476  -8.178  1.00 79.30           N  
+ANISOU 1159  N   GLN B  62    10161  10347   9623   -909    123    751       N  
+ATOM   1160  CA  GLN B  62     -32.867 -24.772  -7.012  1.00 68.13           C  
+ANISOU 1160  CA  GLN B  62     8730   9027   8129   -755    210    719       C  
+ATOM   1161  C   GLN B  62     -33.726 -25.126  -5.824  1.00 70.39           C  
+ANISOU 1161  C   GLN B  62     8983   9467   8294   -906    322    843       C  
+ATOM   1162  O   GLN B  62     -34.807 -25.613  -6.012  1.00 70.22           O  
+ANISOU 1162  O   GLN B  62     8868   9532   8279  -1119    351    940       O  
+ATOM   1163  CB  GLN B  62     -32.896 -23.248  -7.236  1.00 67.38           C  
+ANISOU 1163  CB  GLN B  62     8445   9063   8093   -577    276    593       C  
+ATOM   1164  CG  GLN B  62     -34.246 -22.561  -6.972  1.00 69.55           C  
+ANISOU 1164  CG  GLN B  62     8479   9582   8363   -600    408    617       C  
+ATOM   1165  CD  GLN B  62     -34.463 -22.057  -5.534  1.00 62.14           C  
+ANISOU 1165  CD  GLN B  62     7513   8808   7289   -536    557    618       C  
+ATOM   1166  OE1 GLN B  62     -33.521 -21.731  -4.823  1.00 54.90           O  
+ANISOU 1166  OE1 GLN B  62     6736   7827   6294   -429    553    551       O  
+ATOM   1167  NE2 GLN B  62     -35.725 -21.958  -5.128  1.00 63.75           N  
+ANISOU 1167  NE2 GLN B  62     7519   9253   7449   -599    689    690       N  
+ATOM   1168  N   SER B  63     -33.270 -24.812  -4.615  1.00 70.67           N  
+ANISOU 1168  N   SER B  63     9076   9569   8205   -808    389    839       N  
+ATOM   1169  CA  SER B  63     -34.035 -25.114  -3.403  1.00 75.26           C  
+ANISOU 1169  CA  SER B  63     9643  10319   8633   -940    519    961       C  
+ATOM   1170  C   SER B  63     -33.862 -24.131  -2.248  1.00 70.31           C  
+ANISOU 1170  C   SER B  63     8977   9863   7874   -780    639    888       C  
+ATOM   1171  O   SER B  63     -34.598 -24.210  -1.268  1.00 78.27           O  
+ANISOU 1171  O   SER B  63     9939  11060   8737   -863    783    973       O  
+ATOM   1172  CB  SER B  63     -33.622 -26.492  -2.865  1.00 78.05           C  
+ANISOU 1172  CB  SER B  63    10283  10493   8878  -1077    445   1110       C  
+ATOM   1173  OG  SER B  63     -32.682 -26.352  -1.790  1.00 90.02           O  
+ANISOU 1173  OG  SER B  63    11950  12004  10249   -923    435   1099       O  
+ATOM   1174  N   PHE B  64     -32.871 -23.255  -2.316  1.00 65.41           N  
+ANISOU 1174  N   PHE B  64     8394   9180   7277   -573    583    734       N  
+ATOM   1175  CA  PHE B  64     -32.513 -22.466  -1.160  1.00 66.55           C  
+ANISOU 1175  CA  PHE B  64     8587   9435   7264   -453    656    655       C  
+ATOM   1176  C   PHE B  64     -33.316 -21.199  -1.122  1.00 68.15           C  
+ANISOU 1176  C   PHE B  64     8618   9800   7476   -340    809    543       C  
+ATOM   1177  O   PHE B  64     -33.653 -20.718  -0.042  1.00 74.02           O  
+ANISOU 1177  O   PHE B  64     9375  10700   8049   -284    945    514       O  
+ATOM   1178  CB  PHE B  64     -31.016 -22.107  -1.193  1.00 68.74           C  
+ANISOU 1178  CB  PHE B  64     8990   9582   7543   -323    508    542       C  
+ATOM   1179  CG  PHE B  64     -30.513 -21.437   0.066  1.00 66.26           C  
+ANISOU 1179  CG  PHE B  64     8771   9370   7032   -245    537    461       C  
+ATOM   1180  CD1 PHE B  64     -30.170 -22.204   1.194  1.00 72.14           C  
+ANISOU 1180  CD1 PHE B  64     9675  10158   7576   -288    506    569       C  
+ATOM   1181  CD2 PHE B  64     -30.367 -20.052   0.126  1.00 68.69           C  
+ANISOU 1181  CD2 PHE B  64     9050   9711   7337   -137    581    279       C  
+ATOM   1182  CE1 PHE B  64     -29.710 -21.588   2.347  1.00 71.63           C  
+ANISOU 1182  CE1 PHE B  64     9709  10202   7302   -228    515    487       C  
+ATOM   1183  CE2 PHE B  64     -29.898 -19.430   1.275  1.00 69.45           C  
+ANISOU 1183  CE2 PHE B  64     9273   9885   7231    -91    592    184       C  
+ATOM   1184  CZ  PHE B  64     -29.571 -20.192   2.381  1.00 72.58           C  
+ANISOU 1184  CZ  PHE B  64     9799  10357   7420   -139    555    283       C  
+ATOM   1185  N   LEU B  65     -33.564 -20.610  -2.286  1.00 63.83           N  
+ANISOU 1185  N   LEU B  65     7937   9206   7106   -274    785    473       N  
+ATOM   1186  CA  LEU B  65     -34.355 -19.387  -2.350  1.00 66.16           C  
+ANISOU 1186  CA  LEU B  65     8089   9630   7419   -115    921    375       C  
+ATOM   1187  C   LEU B  65     -35.835 -19.702  -2.078  1.00 70.47           C  
+ANISOU 1187  C   LEU B  65     8411  10440   7921   -180   1083    494       C  
+ATOM   1188  O   LEU B  65     -36.350 -20.690  -2.636  1.00 62.63           O  
+ANISOU 1188  O   LEU B  65     7317   9477   7002   -379   1035    634       O  
+ATOM   1189  CB  LEU B  65     -34.235 -18.733  -3.729  1.00 59.60           C  
+ANISOU 1189  CB  LEU B  65     7191   8674   6779    -25    837    299       C  
+ATOM   1190  CG  LEU B  65     -32.861 -18.246  -4.188  1.00 57.76           C  
+ANISOU 1190  CG  LEU B  65     7120   8221   6602     27    700    183       C  
+ATOM   1191  CD1 LEU B  65     -32.917 -17.582  -5.576  1.00 57.81           C  
+ANISOU 1191  CD1 LEU B  65     7061   8127   6775    102    646    135       C  
+ATOM   1192  CD2 LEU B  65     -32.327 -17.275  -3.169  1.00 54.39           C  
+ANISOU 1192  CD2 LEU B  65     6839   7788   6036    131    752     49       C  
+ATOM   1193  N   ASP B  66     -36.487 -18.860  -1.244  1.00 74.89           N  
+ANISOU 1193  N   ASP B  66     8903  11198   8353    -19   1274    433       N  
+ATOM   1194  CA  ASP B  66     -37.951 -18.868  -1.031  1.00 83.97           C  
+ANISOU 1194  CA  ASP B  66     9768  12675   9461    -11   1464    525       C  
+ATOM   1195  C   ASP B  66     -38.674 -18.077  -2.147  1.00 89.05           C  
+ANISOU 1195  C   ASP B  66    10182  13382  10272    163   1465    482       C  
+ATOM   1196  O   ASP B  66     -38.020 -17.512  -3.028  1.00 82.08           O  
+ANISOU 1196  O   ASP B  66     9403  12261   9520    266   1329    383       O  
+ATOM   1197  CB  ASP B  66     -38.358 -18.435   0.427  1.00 96.74           C  
+ANISOU 1197  CB  ASP B  66    11411  14515  10828    108   1694    490       C  
+ATOM   1198  CG  ASP B  66     -37.950 -16.966   0.829  1.00101.11           C  
+ANISOU 1198  CG  ASP B  66    12141  14972  11304    434   1759    259       C  
+ATOM   1199  OD1 ASP B  66     -37.822 -16.062  -0.014  1.00103.38           O  
+ANISOU 1199  OD1 ASP B  66    12437  15111  11732    617   1698    145       O  
+ATOM   1200  OD2 ASP B  66     -37.801 -16.698   2.048  1.00107.31           O  
+ANISOU 1200  OD2 ASP B  66    13086  15829  11857    502   1880    192       O  
+ATOM   1201  N   ASP B  67     -40.005 -18.040  -2.158  1.00 86.95           N  
+ANISOU 1201  N   ASP B  67     9589  13450   9995    197   1609    569       N  
+ATOM   1202  CA  ASP B  67     -40.677 -17.431  -3.312  1.00 90.53           C  
+ANISOU 1202  CA  ASP B  67     9811  13977  10608    358   1567    559       C  
+ATOM   1203  C   ASP B  67     -40.717 -15.891  -3.254  1.00 86.24           C  
+ANISOU 1203  C   ASP B  67     9333  13386  10046    784   1662    390       C  
+ATOM   1204  O   ASP B  67     -40.642 -15.233  -4.281  1.00 81.53           O  
+ANISOU 1204  O   ASP B  67     8742  12650   9585    940   1557    340       O  
+ATOM   1205  CB  ASP B  67     -42.050 -18.071  -3.552  1.00102.24           C  
+ANISOU 1205  CB  ASP B  67    10878  15858  12109    201   1632    735       C  
+ATOM   1206  CG  ASP B  67     -41.961 -19.594  -3.777  1.00110.12           C  
+ANISOU 1206  CG  ASP B  67    11890  16814  13135   -260   1502    895       C  
+ATOM   1207  OD1 ASP B  67     -41.291 -20.027  -4.737  1.00 98.84           O  
+ANISOU 1207  OD1 ASP B  67    10618  15101  11835   -390   1286    884       O  
+ATOM   1208  OD2 ASP B  67     -42.569 -20.364  -2.992  1.00123.31           O  
+ANISOU 1208  OD2 ASP B  67    13438  18728  14684   -494   1624   1033       O  
+ATOM   1209  N   GLU B  68     -40.822 -15.309  -2.066  1.00 91.45           N  
+ANISOU 1209  N   GLU B  68    10086  14137  10521    974   1859    301       N  
+ATOM   1210  CA  GLU B  68     -40.562 -13.877  -1.887  1.00 92.79           C  
+ANISOU 1210  CA  GLU B  68    10476  14135  10644   1350   1926    105       C  
+ATOM   1211  C   GLU B  68     -39.357 -13.490  -2.763  1.00 88.95           C  
+ANISOU 1211  C   GLU B  68    10277  13221  10296   1308   1700     12       C  
+ATOM   1212  O   GLU B  68     -39.451 -12.586  -3.592  1.00 86.77           O  
+ANISOU 1212  O   GLU B  68    10035  12811  10122   1529   1655    -46       O  
+ATOM   1213  CB  GLU B  68     -40.252 -13.581  -0.409  1.00103.28           C  
+ANISOU 1213  CB  GLU B  68    12042  15476  11725   1425   2090     -9       C  
+ATOM   1214  CG  GLU B  68     -39.658 -12.210  -0.110  1.00110.78           C  
+ANISOU 1214  CG  GLU B  68    13356  16139  12594   1717   2114   -242       C  
+ATOM   1215  CD  GLU B  68     -40.711 -11.114  -0.156  1.00127.27           C  
+ANISOU 1215  CD  GLU B  68    15344  18364  14648   2164   2303   -314       C  
+ATOM   1216  OE1 GLU B  68     -41.594 -11.091   0.736  1.00128.34           O  
+ANISOU 1216  OE1 GLU B  68    15322  18834  14608   2332   2547   -306       O  
+ATOM   1217  OE2 GLU B  68     -40.658 -10.276  -1.086  1.00135.31           O  
+ANISOU 1217  OE2 GLU B  68    16444  19164  15804   2367   2214   -371       O  
+ATOM   1218  N   GLN B  69     -38.246 -14.206  -2.567  1.00 72.49           N  
+ANISOU 1218  N   GLN B  69     8389  10950   8204   1029   1565     15       N  
+ATOM   1219  CA  GLN B  69     -36.950 -13.911  -3.200  1.00 73.21           C  
+ANISOU 1219  CA  GLN B  69     8740  10685   8389    958   1373    -72       C  
+ATOM   1220  C   GLN B  69     -36.830 -14.132  -4.727  1.00 65.48           C  
+ANISOU 1220  C   GLN B  69     7666   9593   7621    882   1203     -2       C  
+ATOM   1221  O   GLN B  69     -36.176 -13.383  -5.439  1.00 63.34           O  
+ANISOU 1221  O   GLN B  69     7557   9080   7428    951   1109    -83       O  
+ATOM   1222  CB  GLN B  69     -35.889 -14.744  -2.517  1.00 75.50           C  
+ANISOU 1222  CB  GLN B  69     9196  10892   8596    710   1285    -63       C  
+ATOM   1223  CG  GLN B  69     -35.602 -14.267  -1.103  1.00 78.45           C  
+ANISOU 1223  CG  GLN B  69     9777  11287   8741    786   1396   -180       C  
+ATOM   1224  CD  GLN B  69     -34.680 -15.215  -0.356  1.00 80.20           C  
+ANISOU 1224  CD  GLN B  69    10125  11490   8855    555   1301   -133       C  
+ATOM   1225  OE1 GLN B  69     -34.695 -16.439  -0.569  1.00 76.67           O  
+ANISOU 1225  OE1 GLN B  69     9569  11099   8460    360   1233     26       O  
+ATOM   1226  NE2 GLN B  69     -33.869 -14.655   0.531  1.00 79.87           N  
+ANISOU 1226  NE2 GLN B  69    10337  11359   8650    578   1283   -273       N  
+ATOM   1227  N   ILE B  70     -37.462 -15.169  -5.220  1.00 61.39           N  
+ANISOU 1227  N   ILE B  70     6901   9247   7174    715   1163    150       N  
+ATOM   1228  CA  ILE B  70     -37.598 -15.345  -6.623  1.00 62.15           C  
+ANISOU 1228  CA  ILE B  70     6889   9291   7432    668   1022    213       C  
+ATOM   1229  C   ILE B  70     -38.394 -14.186  -7.226  1.00 73.71           C  
+ANISOU 1229  C   ILE B  70     8249  10811   8945    974   1070    184       C  
+ATOM   1230  O   ILE B  70     -37.990 -13.601  -8.254  1.00 73.86           O  
+ANISOU 1230  O   ILE B  70     8375  10629   9058   1051    959    151       O  
+ATOM   1231  CB  ILE B  70     -38.275 -16.689  -6.902  1.00 63.18           C  
+ANISOU 1231  CB  ILE B  70     6790   9618   7596    406    976    375       C  
+ATOM   1232  CG1 ILE B  70     -37.310 -17.798  -6.413  1.00 66.78           C  
+ANISOU 1232  CG1 ILE B  70     7440   9927   8005    147    902    402       C  
+ATOM   1233  CG2 ILE B  70     -38.638 -16.782  -8.387  1.00 57.25           C  
+ANISOU 1233  CG2 ILE B  70     5905   8860   6984    377    830    431       C  
+ATOM   1234  CD1 ILE B  70     -37.651 -19.227  -6.791  1.00 70.61           C  
+ANISOU 1234  CD1 ILE B  70     7840  10465   8522   -155    814    547       C  
+ATOM   1235  N   GLY B  71     -39.521 -13.852  -6.588  1.00 75.76           N  
+ANISOU 1235  N   GLY B  71     8304  11355   9126   1166   1244    206       N  
+ATOM   1236  CA  GLY B  71     -40.376 -12.761  -7.036  1.00 72.95           C  
+ANISOU 1236  CA  GLY B  71     7834  11088   8796   1528   1307    188       C  
+ATOM   1237  C   GLY B  71     -39.624 -11.447  -7.147  1.00 76.38           C  
+ANISOU 1237  C   GLY B  71     8635  11163   9222   1770   1297     33       C  
+ATOM   1238  O   GLY B  71     -39.883 -10.642  -8.039  1.00 79.14           O  
+ANISOU 1238  O   GLY B  71     9008  11417   9641   1993   1244     36       O  
+ATOM   1239  N   GLU B  72     -38.660 -11.230  -6.267  1.00 77.34           N  
+ANISOU 1239  N   GLU B  72     9065  11073   9246   1700   1332    -94       N  
+ATOM   1240  CA  GLU B  72     -37.776 -10.071  -6.409  1.00 82.72           C  
+ANISOU 1240  CA  GLU B  72    10132  11378   9918   1818   1290   -240       C  
+ATOM   1241  C   GLU B  72     -36.680 -10.326  -7.459  1.00 73.65           C  
+ANISOU 1241  C   GLU B  72     9106   9983   8893   1567   1086   -215       C  
+ATOM   1242  O   GLU B  72     -35.725  -9.562  -7.537  1.00 70.35           O  
+ANISOU 1242  O   GLU B  72     8999   9266   8462   1543   1035   -321       O  
+ATOM   1243  CB  GLU B  72     -37.154  -9.705  -5.053  1.00 94.77           C  
+ANISOU 1243  CB  GLU B  72    11940  12798  11270   1810   1386   -397       C  
+ATOM   1244  CG  GLU B  72     -38.118  -9.911  -3.884  1.00110.12           C  
+ANISOU 1244  CG  GLU B  72    13720  15060  13058   1957   1598   -397       C  
+ATOM   1245  CD  GLU B  72     -37.932  -8.936  -2.746  1.00125.11           C  
+ANISOU 1245  CD  GLU B  72    15946  16831  14757   2160   1737   -591       C  
+ATOM   1246  OE1 GLU B  72     -38.918  -8.231  -2.409  1.00134.61           O  
+ANISOU 1246  OE1 GLU B  72    17112  18158  15874   2531   1921   -638       O  
+ATOM   1247  OE2 GLU B  72     -36.813  -8.896  -2.185  1.00125.40           O  
+ANISOU 1247  OE2 GLU B  72    16271  16663  14709   1956   1661   -698       O  
+ATOM   1248  N   GLY B  73     -36.799 -11.410  -8.233  1.00 65.49           N  
+ANISOU 1248  N   GLY B  73     7839   9083   7962   1362    977    -81       N  
+ATOM   1249  CA  GLY B  73     -35.815 -11.747  -9.280  1.00 62.64           C  
+ANISOU 1249  CA  GLY B  73     7570   8528   7700   1152    805    -56       C  
+ATOM   1250  C   GLY B  73     -34.511 -12.432  -8.913  1.00 64.69           C  
+ANISOU 1250  C   GLY B  73     7964   8676   7938    882    732    -95       C  
+ATOM   1251  O   GLY B  73     -33.621 -12.552  -9.759  1.00 61.13           O  
+ANISOU 1251  O   GLY B  73     7598   8075   7554    753    615    -91       O  
+ATOM   1252  N   PHE B  74     -34.380 -12.937  -7.687  1.00 63.75           N  
+ANISOU 1252  N   PHE B  74     7851   8656   7716    805    798   -121       N  
+ATOM   1253  CA  PHE B  74     -33.146 -13.627  -7.305  1.00 53.01           C  
+ANISOU 1253  CA  PHE B  74     6598   7217   6322    587    711   -142       C  
+ATOM   1254  C   PHE B  74     -32.988 -14.972  -7.975  1.00 47.15           C  
+ANISOU 1254  C   PHE B  74     5729   6525   5658    405    605    -25       C  
+ATOM   1255  O   PHE B  74     -33.925 -15.691  -8.210  1.00 47.19           O  
+ANISOU 1255  O   PHE B  74     5555   6679   5693    369    619     77       O  
+ATOM   1256  CB  PHE B  74     -33.033 -13.757  -5.799  1.00 57.58           C  
+ANISOU 1256  CB  PHE B  74     7252   7883   6742    571    795   -193       C  
+ATOM   1257  CG  PHE B  74     -32.721 -12.455  -5.116  1.00 62.39           C  
+ANISOU 1257  CG  PHE B  74     8094   8364   7244    697    859   -353       C  
+ATOM   1258  CD1 PHE B  74     -31.451 -11.886  -5.228  1.00 64.10           C  
+ANISOU 1258  CD1 PHE B  74     8521   8379   7455    591    755   -452       C  
+ATOM   1259  CD2 PHE B  74     -33.694 -11.780  -4.360  1.00 68.55           C  
+ANISOU 1259  CD2 PHE B  74     8895   9233   7917    917   1026   -411       C  
+ATOM   1260  CE1 PHE B  74     -31.155 -10.674  -4.606  1.00 68.98           C  
+ANISOU 1260  CE1 PHE B  74     9402   8846   7962    659    796   -610       C  
+ATOM   1261  CE2 PHE B  74     -33.400 -10.578  -3.721  1.00 69.76           C  
+ANISOU 1261  CE2 PHE B  74     9331   9224   7950   1040   1082   -581       C  
+ATOM   1262  CZ  PHE B  74     -32.132 -10.015  -3.852  1.00 73.33           C  
+ANISOU 1262  CZ  PHE B  74    10030   9434   8398    891    957   -683       C  
+ATOM   1263  N   VAL B  75     -31.754 -15.313  -8.293  1.00 47.62           N  
+ANISOU 1263  N   VAL B  75     5890   6460   5740    284    497    -46       N  
+ATOM   1264  CA  VAL B  75     -31.467 -16.527  -9.040  1.00 46.67           C  
+ANISOU 1264  CA  VAL B  75     5712   6336   5685    155    395     39       C  
+ATOM   1265  C   VAL B  75     -30.245 -17.245  -8.471  1.00 44.46           C  
+ANISOU 1265  C   VAL B  75     5526   6018   5347     63    327     28       C  
+ATOM   1266  O   VAL B  75     -29.283 -16.611  -8.088  1.00 45.81           O  
+ANISOU 1266  O   VAL B  75     5789   6141   5474     68    309    -55       O  
+ATOM   1267  CB  VAL B  75     -31.345 -16.225 -10.573  1.00 48.40           C  
+ANISOU 1267  CB  VAL B  75     5921   6459   6009    172    323     45       C  
+ATOM   1268  CG1 VAL B  75     -30.229 -15.219 -10.891  1.00 49.82           C  
+ANISOU 1268  CG1 VAL B  75     6236   6497   6194    190    302    -42       C  
+ATOM   1269  CG2 VAL B  75     -31.192 -17.513 -11.372  1.00 52.32           C  
+ANISOU 1269  CG2 VAL B  75     6386   6945   6547     57    228    117       C  
+ATOM   1270  N   LEU B  76     -30.313 -18.572  -8.356  1.00 47.02           N  
+ANISOU 1270  N   LEU B  76     5836   6371   5658    -24    284    120       N  
+ATOM   1271  CA  LEU B  76     -29.121 -19.328  -8.132  1.00 46.01           C  
+ANISOU 1271  CA  LEU B  76     5797   6192   5492    -56    197    127       C  
+ATOM   1272  C   LEU B  76     -28.512 -19.742  -9.476  1.00 40.71           C  
+ANISOU 1272  C   LEU B  76     5131   5424   4910    -54    113    128       C  
+ATOM   1273  O   LEU B  76     -29.048 -20.600 -10.147  1.00 46.45           O  
+ANISOU 1273  O   LEU B  76     5862   6109   5676   -101     81    191       O  
+ATOM   1274  CB  LEU B  76     -29.384 -20.509  -7.221  1.00 47.02           C  
+ANISOU 1274  CB  LEU B  76     5975   6357   5531   -120    195    227       C  
+ATOM   1275  CG  LEU B  76     -30.003 -20.207  -5.836  1.00 48.21           C  
+ANISOU 1275  CG  LEU B  76     6126   6635   5556   -128    299    239       C  
+ATOM   1276  CD1 LEU B  76     -30.102 -21.517  -5.059  1.00 49.81           C  
+ANISOU 1276  CD1 LEU B  76     6416   6849   5659   -217    281    368       C  
+ATOM   1277  CD2 LEU B  76     -29.254 -19.158  -5.030  1.00 49.77           C  
+ANISOU 1277  CD2 LEU B  76     6382   6864   5663    -57    312    121       C  
+ATOM   1278  N   THR B  77     -27.369 -19.136  -9.812  1.00 41.43           N  
+ANISOU 1278  N   THR B  77     5232   5494   5012    -17     79     55       N  
+ATOM   1279  CA  THR B  77     -26.727 -19.284 -11.128  1.00 40.67           C  
+ANISOU 1279  CA  THR B  77     5128   5343   4981      1     33     43       C  
+ATOM   1280  C   THR B  77     -26.271 -20.689 -11.435  1.00 44.46           C  
+ANISOU 1280  C   THR B  77     5663   5781   5447     32    -31     92       C  
+ATOM   1281  O   THR B  77     -26.273 -21.097 -12.621  1.00 45.14           O  
+ANISOU 1281  O   THR B  77     5776   5802   5573     48    -54     93       O  
+ATOM   1282  CB  THR B  77     -25.599 -18.252 -11.327  1.00 45.56           C  
+ANISOU 1282  CB  THR B  77     5722   5989   5598     -3     32    -32       C  
+ATOM   1283  OG1 THR B  77     -24.616 -18.284 -10.248  1.00 43.74           O  
+ANISOU 1283  OG1 THR B  77     5481   5849   5287    -11     -5    -59       O  
+ATOM   1284  CG2 THR B  77     -26.220 -16.863 -11.400  1.00 41.29           C  
+ANISOU 1284  CG2 THR B  77     5203   5403   5080    -24     94    -78       C  
+ATOM   1285  N   CYS B  78     -25.967 -21.485 -10.393  1.00 45.27           N  
+ANISOU 1285  N   CYS B  78     5822   5901   5476     54    -62    136       N  
+ATOM   1286  CA  CYS B  78     -25.538 -22.878 -10.640  1.00 40.58           C  
+ANISOU 1286  CA  CYS B  78     5341   5220   4856    123   -127    189       C  
+ATOM   1287  C   CYS B  78     -26.708 -23.807 -10.971  1.00 41.12           C  
+ANISOU 1287  C   CYS B  78     5522   5162   4939     26   -135    258       C  
+ATOM   1288  O   CYS B  78     -26.504 -24.884 -11.423  1.00 43.05           O  
+ANISOU 1288  O   CYS B  78     5913   5275   5166     63   -188    285       O  
+ATOM   1289  CB  CYS B  78     -24.806 -23.414  -9.415  1.00 46.97           C  
+ANISOU 1289  CB  CYS B  78     6199   6078   5566    196   -175    233       C  
+ATOM   1290  SG  CYS B  78     -25.953 -23.849  -8.071  1.00 49.40           S  
+ANISOU 1290  SG  CYS B  78     6603   6375   5792     77   -143    334       S  
+ATOM   1291  N   ALA B  79     -27.946 -23.393 -10.780  1.00 44.78           N  
+ANISOU 1291  N   ALA B  79     5918   5669   5425   -101    -84    285       N  
+ATOM   1292  CA  ALA B  79     -29.075 -24.281 -11.005  1.00 47.60           C  
+ANISOU 1292  CA  ALA B  79     6343   5956   5784   -250   -101    364       C  
+ATOM   1293  C   ALA B  79     -30.185 -23.636 -11.871  1.00 49.22           C  
+ANISOU 1293  C   ALA B  79     6406   6233   6061   -337    -80    350       C  
+ATOM   1294  O   ALA B  79     -31.381 -24.008 -11.779  1.00 50.46           O  
+ANISOU 1294  O   ALA B  79     6514   6441   6216   -497    -73    423       O  
+ATOM   1295  CB  ALA B  79     -29.642 -24.689  -9.663  1.00 51.35           C  
+ANISOU 1295  CB  ALA B  79     6846   6483   6181   -345    -59    459       C  
+ATOM   1296  N   ALA B  80     -29.766 -22.691 -12.710  1.00 47.73           N  
+ANISOU 1296  N   ALA B  80     6146   6065   5924   -239    -75    270       N  
+ATOM   1297  CA  ALA B  80     -30.656 -21.820 -13.483  1.00 47.79           C  
+ANISOU 1297  CA  ALA B  80     6019   6149   5986   -255    -60    260       C  
+ATOM   1298  C   ALA B  80     -30.291 -21.968 -14.960  1.00 45.38           C  
+ANISOU 1298  C   ALA B  80     5782   5759   5701   -235   -129    220       C  
+ATOM   1299  O   ALA B  80     -29.179 -21.667 -15.325  1.00 42.72           O  
+ANISOU 1299  O   ALA B  80     5492   5381   5359   -133   -121    162       O  
+ATOM   1300  CB  ALA B  80     -30.480 -20.367 -13.042  1.00 44.94           C  
+ANISOU 1300  CB  ALA B  80     5565   5866   5641   -146     20    209       C  
+ATOM   1301  N   TYR B  81     -31.241 -22.453 -15.772  1.00 45.42           N  
+ANISOU 1301  N   TYR B  81     5782   5764   5709   -349   -198    253       N  
+ATOM   1302  CA  TYR B  81     -31.175 -22.431 -17.214  1.00 43.03           C  
+ANISOU 1302  CA  TYR B  81     5534   5415   5397   -340   -266    217       C  
+ATOM   1303  C   TYR B  81     -31.816 -21.180 -17.774  1.00 44.38           C  
+ANISOU 1303  C   TYR B  81     5553   5705   5604   -286   -255    229       C  
+ATOM   1304  O   TYR B  81     -32.869 -20.780 -17.277  1.00 44.18           O  
+ANISOU 1304  O   TYR B  81     5365   5812   5607   -312   -236    284       O  
+ATOM   1305  CB  TYR B  81     -31.969 -23.595 -17.812  1.00 42.89           C  
+ANISOU 1305  CB  TYR B  81     5610   5343   5342   -522   -376    244       C  
+ATOM   1306  CG  TYR B  81     -31.528 -24.936 -17.365  1.00 42.13           C  
+ANISOU 1306  CG  TYR B  81     5733   5076   5198   -585   -404    245       C  
+ATOM   1307  CD1 TYR B  81     -30.314 -25.445 -17.790  1.00 44.66           C  
+ANISOU 1307  CD1 TYR B  81     6255   5239   5473   -442   -407    173       C  
+ATOM   1308  CD2 TYR B  81     -32.339 -25.734 -16.540  1.00 48.75           C  
+ANISOU 1308  CD2 TYR B  81     6588   5909   6023   -781   -423    329       C  
+ATOM   1309  CE1 TYR B  81     -29.894 -26.718 -17.417  1.00 43.35           C  
+ANISOU 1309  CE1 TYR B  81     6335   4883   5252   -447   -440    177       C  
+ATOM   1310  CE2 TYR B  81     -31.956 -27.041 -16.215  1.00 49.19           C  
+ANISOU 1310  CE2 TYR B  81     6919   5750   6019   -844   -464    343       C  
+ATOM   1311  CZ  TYR B  81     -30.702 -27.516 -16.640  1.00 48.71           C  
+ANISOU 1311  CZ  TYR B  81     7087   5502   5916   -648   -475    264       C  
+ATOM   1312  OH  TYR B  81     -30.184 -28.775 -16.265  1.00 52.95           O  
+ANISOU 1312  OH  TYR B  81     7931   5800   6387   -626   -510    278       O  
+ATOM   1313  N   PRO B  82     -31.222 -20.582 -18.851  1.00 42.24           N  
+ANISOU 1313  N   PRO B  82     5338   5394   5317   -199   -264    189       N  
+ATOM   1314  CA  PRO B  82     -31.916 -19.427 -19.426  1.00 43.63           C  
+ANISOU 1314  CA  PRO B  82     5410   5655   5512   -135   -271    223       C  
+ATOM   1315  C   PRO B  82     -33.193 -19.929 -20.110  1.00 42.47           C  
+ANISOU 1315  C   PRO B  82     5186   5607   5344   -243   -390    277       C  
+ATOM   1316  O   PRO B  82     -33.182 -21.018 -20.729  1.00 43.18           O  
+ANISOU 1316  O   PRO B  82     5392   5637   5378   -371   -481    256       O  
+ATOM   1317  CB  PRO B  82     -30.922 -18.885 -20.482  1.00 44.26           C  
+ANISOU 1317  CB  PRO B  82     5608   5658   5550    -62   -258    186       C  
+ATOM   1318  CG  PRO B  82     -29.978 -19.997 -20.799  1.00 44.00           C  
+ANISOU 1318  CG  PRO B  82     5714   5541   5462    -94   -268    127       C  
+ATOM   1319  CD  PRO B  82     -30.010 -20.955 -19.610  1.00 43.22           C  
+ANISOU 1319  CD  PRO B  82     5616   5415   5388   -148   -264    126       C  
+ATOM   1320  N   THR B  83     -34.264 -19.156 -20.049  1.00 43.35           N  
+ANISOU 1320  N   THR B  83     5114   5871   5484   -188   -400    342       N  
+ATOM   1321  CA  THR B  83     -35.417 -19.426 -20.932  1.00 48.62           C  
+ANISOU 1321  CA  THR B  83     5669   6684   6117   -276   -540    401       C  
+ATOM   1322  C   THR B  83     -35.748 -18.249 -21.876  1.00 46.65           C  
+ANISOU 1322  C   THR B  83     5378   6497   5848   -103   -583    444       C  
+ATOM   1323  O   THR B  83     -36.739 -18.269 -22.580  1.00 52.22           O  
+ANISOU 1323  O   THR B  83     5955   7366   6519   -132   -710    507       O  
+ATOM   1324  CB  THR B  83     -36.648 -19.794 -20.074  1.00 51.91           C  
+ANISOU 1324  CB  THR B  83     5841   7312   6568   -382   -542    472       C  
+ATOM   1325  OG1 THR B  83     -36.869 -18.747 -19.119  1.00 51.49           O  
+ANISOU 1325  OG1 THR B  83     5651   7343   6568   -184   -407    493       O  
+ATOM   1326  CG2 THR B  83     -36.374 -21.131 -19.339  1.00 48.25           C  
+ANISOU 1326  CG2 THR B  83     5482   6756   6094   -602   -531    453       C  
+ATOM   1327  N   SER B  84     -34.922 -17.220 -21.872  1.00 49.15           N  
+ANISOU 1327  N   SER B  84     5810   6685   6177     63   -486    421       N  
+ATOM   1328  CA  SER B  84     -34.968 -16.169 -22.893  1.00 47.46           C  
+ANISOU 1328  CA  SER B  84     5660   6452   5920    210   -525    469       C  
+ATOM   1329  C   SER B  84     -33.560 -15.596 -22.849  1.00 44.74           C  
+ANISOU 1329  C   SER B  84     5522   5905   5571    249   -408    413       C  
+ATOM   1330  O   SER B  84     -32.757 -15.991 -21.985  1.00 42.92           O  
+ANISOU 1330  O   SER B  84     5325   5604   5377    186   -319    344       O  
+ATOM   1331  CB  SER B  84     -35.999 -15.072 -22.468  1.00 52.98           C  
+ANISOU 1331  CB  SER B  84     6195   7271   6664    424   -504    546       C  
+ATOM   1332  OG  SER B  84     -35.478 -14.259 -21.372  1.00 56.24           O  
+ANISOU 1332  OG  SER B  84     6673   7559   7133    543   -346    502       O  
+ATOM   1333  N   ASP B  85     -33.263 -14.621 -23.694  1.00 42.09           N  
+ANISOU 1333  N   ASP B  85     5315   5491   5184    344   -407    456       N  
+ATOM   1334  CA  ASP B  85     -32.096 -13.779 -23.472  1.00 44.39           C  
+ANISOU 1334  CA  ASP B  85     5767   5616   5481    363   -284    426       C  
+ATOM   1335  C   ASP B  85     -32.367 -13.068 -22.174  1.00 44.33           C  
+ANISOU 1335  C   ASP B  85     5710   5574   5557    461   -200    408       C  
+ATOM   1336  O   ASP B  85     -33.473 -12.654 -21.914  1.00 44.74           O  
+ANISOU 1336  O   ASP B  85     5658   5704   5635    607   -226    457       O  
+ATOM   1337  CB  ASP B  85     -31.910 -12.741 -24.580  1.00 50.33           C  
+ANISOU 1337  CB  ASP B  85     6690   6279   6153    434   -297    505       C  
+ATOM   1338  CG  ASP B  85     -31.692 -13.380 -25.963  1.00 53.63           C  
+ANISOU 1338  CG  ASP B  85     7180   6749   6447    352   -376    524       C  
+ATOM   1339  OD1 ASP B  85     -31.204 -14.529 -26.022  1.00 47.82           O  
+ANISOU 1339  OD1 ASP B  85     6425   6053   5688    233   -377    444       O  
+ATOM   1340  OD2 ASP B  85     -32.060 -12.736 -26.984  1.00 54.69           O  
+ANISOU 1340  OD2 ASP B  85     7411   6877   6491    428   -443    619       O  
+ATOM   1341  N   VAL B  86     -31.347 -12.922 -21.361  1.00 40.17           N  
+ANISOU 1341  N   VAL B  86     5253   4953   5056    392   -100    335       N  
+ATOM   1342  CA  VAL B  86     -31.545 -12.627 -20.001  1.00 40.95           C  
+ANISOU 1342  CA  VAL B  86     5304   5044   5208    443    -28    288       C  
+ATOM   1343  C   VAL B  86     -30.338 -11.876 -19.512  1.00 40.30           C  
+ANISOU 1343  C   VAL B  86     5380   4811   5117    374     55    227       C  
+ATOM   1344  O   VAL B  86     -29.225 -12.135 -19.945  1.00 43.19           O  
+ANISOU 1344  O   VAL B  86     5796   5158   5455    238     66    208       O  
+ATOM   1345  CB  VAL B  86     -31.795 -13.954 -19.226  1.00 47.21           C  
+ANISOU 1345  CB  VAL B  86     5933   5975   6029    355    -41    254       C  
+ATOM   1346  CG1 VAL B  86     -30.588 -14.864 -19.281  1.00 53.03           C  
+ANISOU 1346  CG1 VAL B  86     6718   6685   6745    209    -38    201       C  
+ATOM   1347  CG2 VAL B  86     -32.149 -13.690 -17.770  1.00 54.18           C  
+ANISOU 1347  CG2 VAL B  86     6757   6889   6939    415     40    215       C  
+ATOM   1348  N   THR B  87     -30.567 -10.923 -18.633  1.00 40.44           N  
+ANISOU 1348  N   THR B  87     5478   4736   5147    466    116    194       N  
+ATOM   1349  CA  THR B  87     -29.526 -10.137 -17.998  1.00 44.61           C  
+ANISOU 1349  CA  THR B  87     6175   5117   5656    367    180    122       C  
+ATOM   1350  C   THR B  87     -29.555 -10.459 -16.518  1.00 45.83           C  
+ANISOU 1350  C   THR B  87     6259   5336   5818    364    223     34       C  
+ATOM   1351  O   THR B  87     -30.627 -10.480 -15.920  1.00 50.57           O  
+ANISOU 1351  O   THR B  87     6782   6002   6428    521    248     34       O  
+ATOM   1352  CB  THR B  87     -29.811  -8.653 -18.240  1.00 48.52           C  
+ANISOU 1352  CB  THR B  87     6913   5392   6126    483    206    148       C  
+ATOM   1353  OG1 THR B  87     -29.766  -8.415 -19.647  1.00 50.14           O  
+ANISOU 1353  OG1 THR B  87     7196   5550   6304    478    160    251       O  
+ATOM   1354  CG2 THR B  87     -28.775  -7.748 -17.578  1.00 51.37           C  
+ANISOU 1354  CG2 THR B  87     7497   5567   6453    330    258     66       C  
+ATOM   1355  N   ILE B  88     -28.383 -10.757 -15.950  1.00 46.15           N  
+ANISOU 1355  N   ILE B  88     6302   5394   5839    188    231    -31       N  
+ATOM   1356  CA  ILE B  88     -28.248 -11.202 -14.561  1.00 48.38           C  
+ANISOU 1356  CA  ILE B  88     6524   5758   6100    163    252   -105       C  
+ATOM   1357  C   ILE B  88     -27.148 -10.356 -13.868  1.00 49.51           C  
+ANISOU 1357  C   ILE B  88     6821   5800   6187     17    267   -195       C  
+ATOM   1358  O   ILE B  88     -26.006 -10.333 -14.336  1.00 50.31           O  
+ANISOU 1358  O   ILE B  88     6922   5912   6279   -155    240   -192       O  
+ATOM   1359  CB  ILE B  88     -27.854 -12.697 -14.495  1.00 47.16           C  
+ANISOU 1359  CB  ILE B  88     6193   5770   5956     88    209    -84       C  
+ATOM   1360  CG1 ILE B  88     -29.028 -13.550 -14.899  1.00 45.49           C  
+ANISOU 1360  CG1 ILE B  88     5857   5647   5780    178    185    -12       C  
+ATOM   1361  CG2 ILE B  88     -27.449 -13.095 -13.075  1.00 50.06           C  
+ANISOU 1361  CG2 ILE B  88     6533   6211   6275     43    217   -145       C  
+ATOM   1362  CD1 ILE B  88     -28.663 -14.921 -15.331  1.00 44.53           C  
+ANISOU 1362  CD1 ILE B  88     5652   5603   5664    105    128     18       C  
+ATOM   1363  N   GLU B  89     -27.473  -9.703 -12.758  1.00 53.87           N  
+ANISOU 1363  N   GLU B  89     7496   6283   6689     72    309   -278       N  
+ATOM   1364  CA  GLU B  89     -26.437  -9.087 -11.897  1.00 55.06           C  
+ANISOU 1364  CA  GLU B  89     7788   6369   6762   -106    296   -383       C  
+ATOM   1365  C   GLU B  89     -25.875 -10.173 -10.991  1.00 50.59           C  
+ANISOU 1365  C   GLU B  89     7047   6015   6159   -183    255   -407       C  
+ATOM   1366  O   GLU B  89     -26.632 -10.952 -10.372  1.00 53.81           O  
+ANISOU 1366  O   GLU B  89     7350   6536   6558    -58    279   -389       O  
+ATOM   1367  CB  GLU B  89     -26.978  -7.962 -10.983  1.00 64.61           C  
+ANISOU 1367  CB  GLU B  89     9255   7398   7894     -8    353   -489       C  
+ATOM   1368  CG  GLU B  89     -27.906  -6.925 -11.597  1.00 75.35           C  
+ANISOU 1368  CG  GLU B  89    10817   8537   9275    195    408   -466       C  
+ATOM   1369  CD  GLU B  89     -28.548  -5.964 -10.562  1.00 82.40           C  
+ANISOU 1369  CD  GLU B  89    11968   9264  10073    373    485   -588       C  
+ATOM   1370  OE1 GLU B  89     -29.068  -6.404  -9.504  1.00 81.15           O  
+ANISOU 1370  OE1 GLU B  89    11720   9254   9857    488    538   -645       O  
+ATOM   1371  OE2 GLU B  89     -28.574  -4.751 -10.836  1.00 78.16           O  
+ANISOU 1371  OE2 GLU B  89    11754   8436   9505    415    502   -623       O  
+ATOM   1372  N   THR B  90     -24.559 -10.217 -10.878  1.00 51.58           N  
+ANISOU 1372  N   THR B  90     7135   6210   6250   -392    193   -434       N  
+ATOM   1373  CA  THR B  90     -23.886 -11.258 -10.104  1.00 50.76           C  
+ANISOU 1373  CA  THR B  90     6862   6321   6103   -439    132   -438       C  
+ATOM   1374  C   THR B  90     -23.428 -10.795  -8.698  1.00 54.51           C  
+ANISOU 1374  C   THR B  90     7442   6820   6450   -544     93   -549       C  
+ATOM   1375  O   THR B  90     -23.592  -9.656  -8.337  1.00 56.29           O  
+ANISOU 1375  O   THR B  90     7894   6876   6618   -596    118   -640       O  
+ATOM   1376  CB  THR B  90     -22.680 -11.779 -10.880  1.00 51.05           C  
+ANISOU 1376  CB  THR B  90     6727   6500   6170   -558     78   -385       C  
+ATOM   1377  OG1 THR B  90     -21.707 -10.743 -11.014  1.00 54.51           O  
+ANISOU 1377  OG1 THR B  90     7235   6905   6570   -789     55   -432       O  
+ATOM   1378  CG2 THR B  90     -23.111 -12.265 -12.264  1.00 50.66           C  
+ANISOU 1378  CG2 THR B  90     6610   6424   6212   -455    115   -293       C  
+ATOM   1379  N   HIS B  91     -22.903 -11.730  -7.904  1.00 57.41           N  
+ANISOU 1379  N   HIS B  91     7670   7387   6755   -556     26   -538       N  
+ATOM   1380  CA  HIS B  91     -22.350 -11.451  -6.562  1.00 53.16           C  
+ANISOU 1380  CA  HIS B  91     7206   6925   6066   -666    -42   -633       C  
+ATOM   1381  C   HIS B  91     -23.379 -10.865  -5.635  1.00 52.82           C  
+ANISOU 1381  C   HIS B  91     7383   6755   5930   -566     36   -720       C  
+ATOM   1382  O   HIS B  91     -23.140  -9.839  -5.055  1.00 57.23           O  
+ANISOU 1382  O   HIS B  91     8152   7207   6385   -681     21   -845       O  
+ATOM   1383  CB  HIS B  91     -21.120 -10.564  -6.646  1.00 52.81           C  
+ANISOU 1383  CB  HIS B  91     7193   6894   5976   -939   -126   -702       C  
+ATOM   1384  CG  HIS B  91     -19.981 -11.185  -7.409  1.00 56.19           C  
+ANISOU 1384  CG  HIS B  91     7349   7534   6464  -1027   -193   -617       C  
+ATOM   1385  ND1 HIS B  91     -20.029 -11.423  -8.768  1.00 58.74           N  
+ANISOU 1385  ND1 HIS B  91     7574   7829   6914   -972   -131   -528       N  
+ATOM   1386  CD2 HIS B  91     -18.759 -11.596  -7.006  1.00 57.11           C  
+ANISOU 1386  CD2 HIS B  91     7263   7919   6514  -1145   -312   -608       C  
+ATOM   1387  CE1 HIS B  91     -18.883 -11.936  -9.173  1.00 56.30           C  
+ANISOU 1387  CE1 HIS B  91     7023   7755   6612  -1044   -186   -477       C  
+ATOM   1388  NE2 HIS B  91     -18.094 -12.046  -8.123  1.00 61.01           N  
+ANISOU 1388  NE2 HIS B  91     7535   8546   7100  -1142   -299   -520       N  
+ATOM   1389  N   LYS B  92     -24.532 -11.528  -5.533  1.00 51.89           N  
+ANISOU 1389  N   LYS B  92     7218   6656   5842   -359    126   -655       N  
+ATOM   1390  CA  LYS B  92     -25.686 -11.045  -4.764  1.00 55.84           C  
+ANISOU 1390  CA  LYS B  92     7874   7083   6259   -208    243   -719       C  
+ATOM   1391  C   LYS B  92     -25.938 -11.835  -3.472  1.00 58.34           C  
+ANISOU 1391  C   LYS B  92     8162   7572   6430   -160    255   -708       C  
+ATOM   1392  O   LYS B  92     -26.959 -11.637  -2.823  1.00 58.98           O  
+ANISOU 1392  O   LYS B  92     8322   7655   6430    -18    378   -739       O  
+ATOM   1393  CB  LYS B  92     -26.964 -11.067  -5.656  1.00 58.46           C  
+ANISOU 1393  CB  LYS B  92     8144   7346   6720    -12    355   -640       C  
+ATOM   1394  CG  LYS B  92     -26.997  -9.991  -6.743  1.00 61.75           C  
+ANISOU 1394  CG  LYS B  92     8682   7550   7230     -3    369   -662       C  
+ATOM   1395  CD  LYS B  92     -26.411  -8.664  -6.237  1.00 67.88           C  
+ANISOU 1395  CD  LYS B  92     9757   8134   7899   -115    352   -813       C  
+ATOM   1396  CE  LYS B  92     -26.933  -7.436  -6.946  1.00 70.75           C  
+ANISOU 1396  CE  LYS B  92    10351   8225   8305    -10    414   -844       C  
+ATOM   1397  NZ  LYS B  92     -28.067  -6.929  -6.119  1.00 81.14           N  
+ANISOU 1397  NZ  LYS B  92    11822   9481   9525    253    540   -928       N  
+ATOM   1398  N   GLU B  93     -25.011 -12.712  -3.102  1.00 57.86           N  
+ANISOU 1398  N   GLU B  93     7989   7669   6322   -262    135   -655       N  
+ATOM   1399  CA  GLU B  93     -25.136 -13.464  -1.883  1.00 65.82           C  
+ANISOU 1399  CA  GLU B  93     9004   8833   7172   -230    128   -625       C  
+ATOM   1400  C   GLU B  93     -25.494 -12.505  -0.726  1.00 69.11           C  
+ANISOU 1400  C   GLU B  93     9655   9212   7388   -218    194   -777       C  
+ATOM   1401  O   GLU B  93     -26.466 -12.735  -0.015  1.00 63.37           O  
+ANISOU 1401  O   GLU B  93     8970   8546   6562    -93    320   -761       O  
+ATOM   1402  CB  GLU B  93     -23.834 -14.222  -1.595  1.00 65.64           C  
+ANISOU 1402  CB  GLU B  93     8876   8968   7096   -333    -46   -573       C  
+ATOM   1403  CG  GLU B  93     -23.788 -14.779  -0.175  1.00 79.13           C  
+ANISOU 1403  CG  GLU B  93    10652  10826   8585   -318    -84   -555       C  
+ATOM   1404  CD  GLU B  93     -22.987 -16.055  -0.039  1.00 76.96           C  
+ANISOU 1404  CD  GLU B  93    10243  10705   8292   -298   -222   -415       C  
+ATOM   1405  OE1 GLU B  93     -21.780 -16.023  -0.371  1.00 79.66           O  
+ANISOU 1405  OE1 GLU B  93    10469  11135   8663   -371   -367   -426       O  
+ATOM   1406  OE2 GLU B  93     -23.601 -17.080   0.373  1.00 67.00           O  
+ANISOU 1406  OE2 GLU B  93     8994   9478   6985   -203   -176   -287       O  
+ATOM   1407  N   GLU B  94     -24.725 -11.432  -0.566  1.00 69.03           N  
+ANISOU 1407  N   GLU B  94     9811   9108   7309   -360    117   -926       N  
+ATOM   1408  CA  GLU B  94     -24.928 -10.483   0.552  1.00 77.95           C  
+ANISOU 1408  CA  GLU B  94    11229  10170   8216   -366    159  -1102       C  
+ATOM   1409  C   GLU B  94     -26.428 -10.119   0.763  1.00 81.07           C  
+ANISOU 1409  C   GLU B  94    11734  10485   8584   -108    385  -1134       C  
+ATOM   1410  O   GLU B  94     -26.904 -10.013   1.908  1.00 85.54           O  
+ANISOU 1410  O   GLU B  94    12445  11120   8935    -23    471  -1211       O  
+ATOM   1411  CB  GLU B  94     -24.036  -9.252   0.313  1.00 87.19           C  
+ANISOU 1411  CB  GLU B  94    12594  11164   9368   -580     56  -1254       C  
+ATOM   1412  CG  GLU B  94     -24.432  -7.953   1.012  1.00106.45           C  
+ANISOU 1412  CG  GLU B  94    15427  13387  11633   -560    129  -1466       C  
+ATOM   1413  CD  GLU B  94     -23.735  -7.773   2.341  1.00110.68           C  
+ANISOU 1413  CD  GLU B  94    16139  14025  11889   -732      8  -1602       C  
+ATOM   1414  OE1 GLU B  94     -22.649  -8.362   2.521  1.00117.37           O  
+ANISOU 1414  OE1 GLU B  94    16802  15085  12706   -936   -180  -1543       O  
+ATOM   1415  OE2 GLU B  94     -24.273  -7.047   3.196  1.00115.53           O  
+ANISOU 1415  OE2 GLU B  94    17075  14520  12301   -644     98  -1769       O  
+ATOM   1416  N   ALA B  95     -27.170  -9.967  -0.337  1.00 78.47           N  
+ANISOU 1416  N   ALA B  95    11311  10048   8454     26    480  -1068       N  
+ATOM   1417  CA  ALA B  95     -28.574  -9.572  -0.290  1.00 77.65           C  
+ANISOU 1417  CA  ALA B  95    11250   9907   8344    296    683  -1084       C  
+ATOM   1418  C   ALA B  95     -29.499 -10.685   0.182  1.00 81.60           C  
+ANISOU 1418  C   ALA B  95    11531  10661   8809    409    797   -947       C  
+ATOM   1419  O   ALA B  95     -30.560 -10.398   0.728  1.00 86.75           O  
+ANISOU 1419  O   ALA B  95    12220  11380   9361    612    978   -982       O  
+ATOM   1420  CB  ALA B  95     -29.025  -9.052  -1.654  1.00 73.64           C  
+ANISOU 1420  CB  ALA B  95    10698   9230   8050    400    717  -1040       C  
+ATOM   1421  N   ILE B  96     -29.102 -11.941  -0.054  1.00 86.66           N  
+ANISOU 1421  N   ILE B  96    11957  11441   9527    280    698   -787       N  
+ATOM   1422  CA  ILE B  96     -29.871 -13.143   0.330  1.00 86.56           C  
+ANISOU 1422  CA  ILE B  96    11762  11641   9485    314    780   -627       C  
+ATOM   1423  C   ILE B  96     -29.477 -13.617   1.721  1.00 84.77           C  
+ANISOU 1423  C   ILE B  96    11641  11556   9011    242    759   -633       C  
+ATOM   1424  O   ILE B  96     -29.685 -14.761   2.056  1.00 83.12           O  
+ANISOU 1424  O   ILE B  96    11324  11491   8764    195    764   -478       O  
+ATOM   1425  CB  ILE B  96     -29.623 -14.323  -0.663  1.00 90.19           C  
+ANISOU 1425  CB  ILE B  96    12007  12122  10139    213    673   -451       C  
+ATOM   1426  CG1 ILE B  96     -30.006 -13.941  -2.082  1.00 90.30           C  
+ANISOU 1426  CG1 ILE B  96    11917  12018  10374    272    679   -433       C  
+ATOM   1427  CG2 ILE B  96     -30.408 -15.587  -0.291  1.00 96.15           C  
+ANISOU 1427  CG2 ILE B  96    12623  13049  10858    195    743   -278       C  
+ATOM   1428  CD1 ILE B  96     -31.453 -13.513  -2.211  1.00 91.73           C  
+ANISOU 1428  CD1 ILE B  96    12017  12259  10577    456    854   -422       C  
+ATOM   1429  N   MET B  97     -28.867 -12.760   2.519  1.00 96.04           N  
+ANISOU 1429  N   MET B  97    13305  12930  10255    212    718   -806       N  
+ATOM   1430  CA  MET B  97     -28.752 -13.030   3.959  1.00108.10           C  
+ANISOU 1430  CA  MET B  97    14968  14612  11491    186    733   -832       C  
+ATOM   1431  C   MET B  97     -29.333 -11.852   4.784  1.00112.54           C  
+ANISOU 1431  C   MET B  97    15786  15132  11839    327    893  -1037       C  
+ATOM   1432  O   MET B  97     -30.047 -12.090   5.759  1.00113.07           O  
+ANISOU 1432  O   MET B  97    15896  15370  11696    422   1051  -1023       O  
+ATOM   1433  CB  MET B  97     -27.301 -13.410   4.291  1.00103.41           C  
+ANISOU 1433  CB  MET B  97    14414  14054  10823     -6    483   -827       C  
+ATOM   1434  CG  MET B  97     -26.722 -14.327   3.206  1.00102.45           C  
+ANISOU 1434  CG  MET B  97    14057  13920  10946    -76    347   -664       C  
+ATOM   1435  SD  MET B  97     -25.246 -15.322   3.559  1.00117.34           S  
+ANISOU 1435  SD  MET B  97    15877  15943  12762   -203     84   -561       S  
+ATOM   1436  CE  MET B  97     -24.043 -14.027   3.907  1.00103.96           C  
+ANISOU 1436  CE  MET B  97    14327  14224  10946   -367    -80   -786       C  
+ATOM   1437  N   LEU B  98     -29.087 -10.604   4.344  1.00119.26           N  
+ANISOU 1437  N   LEU B  98    16822  15748  12742    354    871  -1217       N  
+ATOM   1438  CA  LEU B  98     -29.639  -9.356   4.952  1.00123.66           C  
+ANISOU 1438  CA  LEU B  98    17689  16180  13115    531   1024  -1437       C  
+ATOM   1439  C   LEU B  98     -30.866  -9.535   5.875  1.00124.53           C  
+ANISOU 1439  C   LEU B  98    17792  16500  13023    769   1286  -1430       C  
+ATOM   1440  O   LEU B  98     -32.001  -9.708   5.420  1.00113.44           O  
+ANISOU 1440  O   LEU B  98    16173  15192  11737    973   1471  -1329       O  
+ATOM   1441  CB  LEU B  98     -29.945  -8.322   3.862  1.00113.25           C  
+ANISOU 1441  CB  LEU B  98    16446  14588  11996    658   1065  -1512       C  
+TER    1442      LEU B  98                                                      
+HETATM 1443 FE1  FES A 201     -15.271 -14.172 -26.506  1.00 44.84          FE  
+ANISOU 1443 FE1  FES A 201     6513   5131   5392   -266   1479   -131      FE  
+HETATM 1444 FE2  FES A 201     -13.886 -13.246 -28.774  1.00 43.12          FE  
+ANISOU 1444 FE2  FES A 201     6178   4976   5230   -316   1145   -235      FE  
+HETATM 1445  S1  FES A 201     -13.297 -13.107 -26.664  1.00 54.52           S  
+ANISOU 1445  S1  FES A 201     7773   6436   6506    -96   1188   -102       S  
+HETATM 1446  S2  FES A 201     -15.933 -14.020 -28.613  1.00 59.15           S  
+ANISOU 1446  S2  FES A 201     8119   7001   7354   -510   1368   -300       S  
+HETATM 1447 CL    CL A 202      -7.271  -6.453 -50.333  1.00 66.75          CL  
+ANISOU 1447 CL    CL A 202     8476   9756   7127    -15    320    384      CL  
+HETATM 1448 FE1  FES B 201     -24.764 -23.326  -3.870  1.00 41.78          FE  
+ANISOU 1448 FE1  FES B 201     5702   5769   4400    126   -205    391      FE  
+HETATM 1449 FE2  FES B 201     -25.332 -22.283  -6.421  1.00 37.10          FE  
+ANISOU 1449 FE2  FES B 201     4925   5056   4113     76   -116    248      FE  
+HETATM 1450  S1  FES B 201     -23.427 -22.583  -5.443  1.00 50.74           S  
+ANISOU 1450  S1  FES B 201     6641   6936   5699    218   -266    253       S  
+HETATM 1451  S2  FES B 201     -26.631 -22.784  -4.792  1.00 52.36           S  
+ANISOU 1451  S2  FES B 201     6974   7030   5890    -29    -34    366       S  
+HETATM 1452 CL    CL B 202     -35.655 -14.036 -25.892  1.00 63.11          CL  
+ANISOU 1452 CL    CL B 202     7828   8449   7699    533   -737    677      CL  
+HETATM 1453  O   HOH A 301      -5.604   9.621 -30.726  1.00 71.67           O  
+ANISOU 1453  O   HOH A 301     9741   6570  10921   -503   1286  -1155       O  
+HETATM 1454  O   HOH A 302      -9.976  -2.053 -46.606  1.00 60.80           O  
+ANISOU 1454  O   HOH A 302     7211   8696   7192    404    154    904       O  
+HETATM 1455  O   HOH A 303     -25.242 -15.543 -37.047  1.00 85.19           O  
+ANISOU 1455  O   HOH A 303     9346  12270  10750  -2562    894  -1311       O  
+HETATM 1456  O   HOH A 304      -8.615  -1.310 -44.946  1.00 51.68           O  
+ANISOU 1456  O   HOH A 304     6188   7004   6442    421    264    856       O  
+HETATM 1457  O   HOH A 305      -6.495 -20.103 -36.227  1.00 66.33           O  
+ANISOU 1457  O   HOH A 305     9914   6783   8504   -320   2093   -239       O  
+HETATM 1458  O   HOH A 306     -15.756 -22.203 -33.220  1.00 75.41           O  
+ANISOU 1458  O   HOH A 306    10813   7895   9944  -1695   2618   -965       O  
+HETATM 1459  O   HOH A 307     -29.136  -5.336 -24.489  1.00 68.01           O  
+ANISOU 1459  O   HOH A 307     7381   9218   9240    419   2448    230       O  
+HETATM 1460  O   HOH A 308     -31.273  -2.568 -37.684  1.00 80.28           O  
+ANISOU 1460  O   HOH A 308     6166  13841  10493    472    476   1418       O  
+HETATM 1461  O   HOH A 309     -12.248  -4.951 -30.108  1.00 43.84           O  
+ANISOU 1461  O   HOH A 309     5908   5247   5501      5    448   -372       O  
+HETATM 1462  O   HOH A 310       1.254  -8.613 -35.928  1.00 55.59           O  
+ANISOU 1462  O   HOH A 310     7059   6744   7319    249    231    444       O  
+HETATM 1463  O   HOH A 311     -14.907  -5.701 -24.000  1.00 59.32           O  
+ANISOU 1463  O   HOH A 311     8290   7265   6981    168    940   -557       O  
+HETATM 1464  O   HOH A 312     -10.817  -7.018 -29.284  1.00 41.62           O  
+ANISOU 1464  O   HOH A 312     5784   4984   5045    -27    423   -341       O  
+HETATM 1465  O   HOH A 313       2.334  -6.045 -37.941  1.00 48.64           O  
+ANISOU 1465  O   HOH A 313     5952   5811   6716    139    202    488       O  
+HETATM 1466  O   HOH A 314     -15.179  -4.981 -27.668  1.00 53.48           O  
+ANISOU 1466  O   HOH A 314     7171   6503   6643     87    768   -437       O  
+HETATM 1467  O   HOH A 315      -0.012 -13.050 -38.710  1.00 53.80           O  
+ANISOU 1467  O   HOH A 315     7374   6131   6936    327    934    389       O  
+HETATM 1468  O   HOH A 316      -4.588   7.953 -34.979  1.00 55.02           O  
+ANISOU 1468  O   HOH A 316     7176   4879   8848   -164   1054   -241       O  
+HETATM 1469  O   HOH A 317      -7.401   1.030 -46.099  1.00 71.07           O  
+ANISOU 1469  O   HOH A 317     8592   9256   9152    695    478   1286       O  
+HETATM 1470  O   HOH B 301     -17.227  -5.370 -20.274  1.00 67.76           O  
+ANISOU 1470  O   HOH B 301     9358   8307   8078  -2373    512    237       O  
+HETATM 1471  O   HOH B 302     -16.773 -19.622 -11.270  1.00 63.07           O  
+ANISOU 1471  O   HOH B 302     7080   9333   7548    271   -261    -62       O  
+HETATM 1472  O   HOH B 303     -33.187 -25.431 -12.986  1.00 63.64           O  
+ANISOU 1472  O   HOH B 303     8214   8071   7895   -876   -197    526       O  
+HETATM 1473  O   HOH B 304     -33.633 -10.672 -27.113  1.00 59.09           O  
+ANISOU 1473  O   HOH B 304     8015   7375   7058    804   -526    819       O  
+HETATM 1474  O   HOH B 305     -29.987  -6.037  -4.511  1.00 66.34           O  
+ANISOU 1474  O   HOH B 305    10207   7566   7433    765    801  -1097       O  
+HETATM 1475  O   HOH B 306     -13.899 -20.518 -11.569  1.00 81.57           O  
+ANISOU 1475  O   HOH B 306     8854  12357   9778    587   -327     -7       O  
+HETATM 1476  O   HOH B 307     -22.312 -17.195  -9.418  1.00 47.15           O  
+ANISOU 1476  O   HOH B 307     5812   6486   5616   -124    -89   -163       O  
+HETATM 1477  O   HOH B 308     -34.144 -23.559 -20.590  1.00 51.64           O  
+ANISOU 1477  O   HOH B 308     6612   6627   6378   -778   -651    271       O  
+HETATM 1478  O   HOH B 309     -24.795 -27.082 -17.164  1.00 48.12           O  
+ANISOU 1478  O   HOH B 309     7064   5473   5745    466   -276     10       O  
+HETATM 1479  O   HOH B 310     -32.217 -13.054   4.356  1.00 88.41           O  
+ANISOU 1479  O   HOH B 310    12239  12424   8929    628   1337   -721       O  
+HETATM 1480  O   HOH B 311     -23.165 -14.400  -5.121  1.00 48.01           O  
+ANISOU 1480  O   HOH B 311     6333   6580   5329   -351    -63   -448       O  
+HETATM 1481  O   HOH B 312     -20.108 -19.770 -22.685  1.00 54.43           O  
+ANISOU 1481  O   HOH B 312     6815   7445   6419    397    344   -109       O  
+HETATM 1482  O   HOH B 313     -29.379 -10.101 -22.915  1.00 62.52           O  
+ANISOU 1482  O   HOH B 313     8624   7375   7757    322     17    426       O  
+HETATM 1483  O   HOH B 314     -23.815 -23.224 -24.077  1.00 46.69           O  
+ANISOU 1483  O   HOH B 314     6623   5782   5333    479     -2   -224       O  
+HETATM 1484  O   HOH B 315     -31.917  -9.402 -21.408  1.00 63.89           O  
+ANISOU 1484  O   HOH B 315     8654   7581   8038    758    -17    436       O  
+HETATM 1485  O   HOH B 316     -43.034 -22.451  -5.025  1.00 82.32           O  
+ANISOU 1485  O   HOH B 316     8131  13423   9723  -1213   1232   1263       O  
+HETATM 1486  O   HOH B 317     -13.942 -19.466 -15.267  1.00 82.69           O  
+ANISOU 1486  O   HOH B 317     8966  12435  10017    416     49    -55       O  
+HETATM 1487  O   HOH B 318     -23.364 -14.585  -8.816  1.00 50.88           O  
+ANISOU 1487  O   HOH B 318     6512   6761   6060   -288     14   -313       O  
+HETATM 1488  O   HOH B 319     -41.794 -18.985   0.026  0.50 60.91           O  
+ANISOU 1488  O   HOH B 319     5945  10874   6323     -9   2050    811       O  
+HETATM 1489  O   HOH B 320     -29.672 -24.828 -29.742  1.00 55.49           O  
+ANISOU 1489  O   HOH B 320     8618   6605   5859   -263   -781   -333       O  
+HETATM 1490  O   HOH B 321     -38.215 -20.833 -12.380  1.00 58.66           O  
+ANISOU 1490  O   HOH B 321     6197   8706   7384   -584    159    654       O  
+CONECT  301 1443                                                                
+CONECT  333 1443                                                                
+CONECT  351 1444                                                                
+CONECT  569 1444                                                                
+CONECT 1022 1448                                                                
+CONECT 1054 1448                                                                
+CONECT 1072 1449                                                                
+CONECT 1290 1449                                                                
+CONECT 1443  301  333 1445 1446                                                 
+CONECT 1444  351  569 1445 1446                                                 
+CONECT 1445 1443 1444                                                           
+CONECT 1446 1443 1444                                                           
+CONECT 1448 1022 1054 1450 1451                                                 
+CONECT 1449 1072 1290 1450 1451                                                 
+CONECT 1450 1448 1449                                                           
+CONECT 1451 1448 1449                                                           
+MASTER      410    0    4    7   14    0    6    6 1488    2   16   18          
+END                                                                             
diff --git a/test/jalview/ext/rbvi/chimera/4zho.xml.gz b/test/jalview/ext/rbvi/chimera/4zho.xml.gz
new file mode 100644
index 0000000..c7e6bd2
Binary files /dev/null and b/test/jalview/ext/rbvi/chimera/4zho.xml.gz differ
diff --git a/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java b/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
new file mode 100644
index 0000000..c9e1cad
--- /dev/null
+++ b/test/jalview/ext/rbvi/chimera/AtomSpecModelTest.java
@@ -0,0 +1,34 @@
+package jalview.ext.rbvi.chimera;
+
+import static org.testng.Assert.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class AtomSpecModelTest
+{
+  @Test(groups = "Functional")
+  public void testGetAtomSpec()
+  {
+    AtomSpecModel model = new AtomSpecModel();
+    assertEquals(model.getAtomSpec(), "");
+    model.addRange(1, 2, 4, "A");
+    assertEquals(model.getAtomSpec(), "#1:2-4.A");
+    model.addRange(1, 8, 8, "A");
+    assertEquals(model.getAtomSpec(), "#1:2-4.A,8.A");
+    model.addRange(1, 5, 7, "B");
+    assertEquals(model.getAtomSpec(), "#1:2-4.A,8.A,5-7.B");
+    model.addRange(1, 3, 5, "A");
+    assertEquals(model.getAtomSpec(), "#1:2-5.A,8.A,5-7.B");
+    model.addRange(0, 1, 4, "B");
+    assertEquals(model.getAtomSpec(), "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
+    model.addRange(0, 5, 9, "C");
+    assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
+    model.addRange(1, 8, 10, "B");
+    assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+    model.addRange(1, 8, 9, "B");
+    assertEquals(model.getAtomSpec(), "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+    model.addRange(0, 3, 10, "C"); // subsumes 5-9
+    assertEquals(model.getAtomSpec(), "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
+  }
+
+}
diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
index ffb886c..2c973ca 100644
--- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
+++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java
@@ -20,17 +20,27 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
-
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceRenderer;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureMappingcommandSet;
+import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
-import java.util.Arrays;
+import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.SortedMap;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -46,58 +56,10 @@ public class ChimeraCommandsTest
   }
 
   @Test(groups = { "Functional" })
-  public void testAddColourRange()
-  {
-    Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
-    ChimeraCommands.addColourRange(map, Color.pink, 1, 2, 4, "A");
-    ChimeraCommands.addColourRange(map, Color.pink, 1, 8, 8, "A");
-    ChimeraCommands.addColourRange(map, Color.pink, 1, 5, 7, "B");
-    ChimeraCommands.addColourRange(map, Color.red, 1, 3, 5, "A");
-    ChimeraCommands.addColourRange(map, Color.red, 0, 1, 4, "B");
-    ChimeraCommands.addColourRange(map, Color.orange, 0, 5, 9, "C");
-
-    // three colours mapped
-    assertEquals(3, map.keySet().size());
-
-    // Red has two models, Pink and Orange one each
-    assertEquals(2, map.get(Color.red).keySet().size());
-    assertEquals(1, map.get(Color.orange).keySet().size());
-    assertEquals(1, map.get(Color.pink).keySet().size());
-
-    // pink model 1 has two chains, red.0 / red.1 / orange.0 one each
-    assertEquals(2, map.get(Color.pink).get(1).keySet().size());
-    assertEquals(1, map.get(Color.red).get(0).keySet().size());
-    assertEquals(1, map.get(Color.red).get(1).keySet().size());
-    assertEquals(1, map.get(Color.orange).get(0).keySet().size());
-
-    // inspect positions
-    List<int[]> posList = map.get(Color.pink).get(1).get("A");
-    assertEquals(2, posList.size());
-    assertTrue(Arrays.equals(new int[] { 2, 4 }, posList.get(0)));
-    assertTrue(Arrays.equals(new int[] { 8, 8 }, posList.get(1)));
-
-    posList = map.get(Color.pink).get(1).get("B");
-    assertEquals(1, posList.size());
-    assertTrue(Arrays.equals(new int[] { 5, 7 }, posList.get(0)));
-
-    posList = map.get(Color.red).get(0).get("B");
-    assertEquals(1, posList.size());
-    assertTrue(Arrays.equals(new int[] { 1, 4 }, posList.get(0)));
-
-    posList = map.get(Color.red).get(1).get("A");
-    assertEquals(1, posList.size());
-    assertTrue(Arrays.equals(new int[] { 3, 5 }, posList.get(0)));
-
-    posList = map.get(Color.orange).get(0).get("C");
-    assertEquals(1, posList.size());
-    assertTrue(Arrays.equals(new int[] { 5, 9 }, posList.get(0)));
-  }
-
-  @Test(groups = { "Functional" })
   public void testBuildColourCommands()
   {
 
-    Map<Color, SortedMap<Integer, Map<String, List<int[]>>>> map = new LinkedHashMap<Color, SortedMap<Integer, Map<String, List<int[]>>>>();
+    Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
     ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
     ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
     ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
@@ -106,13 +68,153 @@ public class ChimeraCommandsTest
     ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
     ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
     ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
+    ChimeraCommands.addColourRange(map, Color.red, 0, 6, 9, "A");
 
     // Colours should appear in the Chimera command in the order in which
-    // they were added; within colour, by model, by chain, and positions as
-    // added
+    // they were added; within colour, by model, by chain, ranges in start order
     String command = ChimeraCommands.buildColourCommands(map).get(0);
     assertEquals(
-            "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:8.A,3-5.A; color #ff0000 #0:3-5.A",
-            command);
+            command,
+            "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testBuildSetAttributeCommands()
+  {
+    /*
+     * make a map of { featureType, {featureValue, {residue range specification } } }
+     */
+    Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
+    Map<Object, AtomSpecModel> featureValues = new HashMap<Object, AtomSpecModel>();
+    
+    /*
+     * start with just one feature/value...
+     */
+    featuresMap.put("chain", featureValues);
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 8, 20, "A");
+  
+    List<String> commands = ChimeraCommands
+            .buildSetAttributeCommands(featuresMap);
+    assertEquals(1, commands.size());
+
+    /*
+     * feature name gets a jv_ namespace prefix
+     * feature value is quoted in case it contains spaces
+     */
+    assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:8-20.A");
+
+    // add same feature value, overlapping range
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 3, 9, "A");
+    // same feature value, contiguous range
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "A");
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertEquals(1, commands.size());
+    assertEquals(commands.get(0), "setattr r jv_chain 'X' #0:3-25.A");
+
+    // same feature value and model, different chain
+    ChimeraCommands.addColourRange(featureValues, "X", 0, 21, 25, "B");
+    // same feature value and chain, different model
+    ChimeraCommands.addColourRange(featureValues, "X", 1, 26, 30, "A");
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertEquals(1, commands.size());
+    assertEquals(commands.get(0),
+            "setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
+
+    // same feature, different value
+    ChimeraCommands.addColourRange(featureValues, "Y", 0, 40, 50, "A");
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertEquals(2, commands.size());
+    // commands are ordered by feature type but not by value
+    // so use contains to test for the expected command:
+    assertTrue(commands
+            .contains("setattr r jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A"));
+    assertTrue(commands.contains("setattr r jv_chain 'Y' #0:40-50.A"));
+
+    featuresMap.clear();
+    featureValues.clear();
+    featuresMap.put("side-chain binding!", featureValues);
+    ChimeraCommands.addColourRange(featureValues,
+            "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
+            "A");
+    // feature names are sanitised to change non-alphanumeric to underscore
+    // feature values are sanitised to encode single quote characters
+    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
+    assertTrue(commands
+            .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' #0:7-15.A"));
+  }
+
+  /**
+   * Tests for the method that prefixes and sanitises a feature name so it can
+   * be used as a valid, namespaced attribute name in Chimera
+   */
+  @Test(groups = { "Functional" })
+  public void testMakeAttributeName()
+  {
+    assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
+    assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
+    assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
+    assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
+            "jv_Hello_World_24");
+    assertEquals(
+            ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
+            "jv__this_is_a_very__odd_name");
+    // name ending in color gets underscore appended
+    assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
+            "jv_helixColor_");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetColourBySequenceCommands_hiddenColumns()
+  {
+    /*
+     * load these sequences, coloured by Strand propensity,
+     * with columns 2-4 hidden
+     */
+    SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
+    SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignFrame af = new AlignFrame(al, 800, 500);
+    af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(2);
+    cs.addElement(3);
+    cs.addElement(4);
+    af.getViewport().setColumnSelection(cs);
+    af.hideSelColumns_actionPerformed(null);
+    SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+    SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
+    String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
+    StructureSelectionManager ssm = new StructureSelectionManager();
+
+    /*
+     * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
+     */
+    HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+    for (int pos = 1; pos <= seq1.getLength(); pos++)
+    {
+      map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
+    }
+    StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
+            "A", map, null);
+    ssm.addStructureMapping(sm1);
+    StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
+            "B", map, null);
+    ssm.addStructureMapping(sm2);
+
+    StructureMappingcommandSet[] commands = ChimeraCommands
+            .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+    assertEquals(1, commands.length);
+    assertEquals(1, commands[0].commands.length);
+    String theCommand = commands[0].commands[0];
+    // M colour is #82827d (see strand.html help page)
+    assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
+    // H colour is #60609f
+    assertTrue(theCommand.contains("color #60609f #0:22.A"));
+    // V colour is #ffff00
+    assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
+    // hidden columns are Gray (128, 128, 128)
+    assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
+    // S and G are both coloured #4949b6
+    assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
   }
 }
diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index f4fb40b..d85bb10 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -20,20 +20,40 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
 
+import jalview.api.FeatureRenderer;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.FileLoader;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.ws.sifts.SiftsClient;
+import jalview.ws.sifts.SiftsException;
+import jalview.ws.sifts.SiftsSettings;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Vector;
 import jalview.io.DataSourceType;
 
 import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -48,15 +68,25 @@ public class JalviewChimeraView
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  private JalviewStructureDisplayI chimeraViewer;
+
   /**
    * @throws java.lang.Exception
    */
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] {
-        "-noquestionnaire -nonews -props",
+    Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
         "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.CHIMERA.name());
+    Cache.setProperty("SHOW_ANNOTATIONS", "false");
+    Cache.setProperty(Preferences.STRUCT_FROM_PDB, "false");
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.CHIMERA.name());
+    Cache.setProperty("MAP_WITH_SIFTS", "true");
+    // TODO this should not be necessary!
+    SiftsSettings.setMapWithSifts(true);
   }
 
   /**
@@ -65,57 +95,388 @@ public class JalviewChimeraView
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @AfterMethod(alwaysRun = true)
+  public void tearDownAfterTest() throws Exception
+  {
+    SiftsClient.setMockSiftsFile(null);
+    if (chimeraViewer != null)
+    {
+      chimeraViewer.closeViewer(true);
+    }
   }
 
-  @Test(groups = { "Functional" })
+  /**
+   * Load 1GAQ and view the first structure for which a PDB id is found. Note no
+   * network connection is needed - PDB file is read locally, SIFTS fetch fails
+   * so mapping falls back to Needleman-Wunsch - ok for this test.
+   */
+  // External as local install of Chimera required
+  @Test(groups = { "External" })
   public void testSingleSeqViewChimera()
   {
-    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
-            ViewerType.CHIMERA.name());
     String inFile = "examples/1gaq.txt";
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, DataSourceType.FILE);
-    assertTrue("Didn't read input file " + inFile, af != null);
-    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Failed to create AlignFrame");
+    SequenceI sq = af.getViewport().getAlignment().getSequenceAt(0);
+    assertEquals(sq.getName(), "1GAQ|A");
+    SequenceI dsq = sq.getDatasetSequence();
+    Vector<PDBEntry> pdbIds = dsq.getAllPDBEntries();
+    assertEquals(pdbIds.size(), 1);
+    PDBEntry pdbEntry = pdbIds.get(0);
+    assertEquals(pdbEntry.getId(), "1GAQ");
+    StructureViewer structureViewer = new StructureViewer(af.getViewport()
+            .getStructureSelectionManager());
+    chimeraViewer = structureViewer.viewStructures(pdbEntry,
+            new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+    JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
+            .getBinding();
+
+    /*
+     * Wait for viewer load thread to complete
+     */
+    while (!binding.isFinishedInit())
     {
-      System.out.println("** sq=" + sq.getName());
-      SequenceI dsq = sq.getDatasetSequence();
-      while (dsq.getDatasetSequence() != null)
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
       {
-        dsq = dsq.getDatasetSequence();
       }
-      if (dsq.getAllPDBEntries() != null
-              && dsq.getAllPDBEntries().size() > 0)
+    }
+
+    assertTrue(binding.isChimeraRunning(), "Failed to start Chimera");
+
+    assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
+    chimeraViewer.closeViewer(true);
+    chimeraViewer = null;
+    return;
+  }
+
+  /**
+   * Test for writing Jalview features as attributes on mapped residues in
+   * Chimera. Note this uses local copies of PDB and SIFTS file, no network
+   * connection required.
+   * 
+   * @throws IOException
+   * @throws SiftsException
+   */
+  // External as this requires a local install of Chimera
+  @Test(groups = { "External" })
+  public void testTransferFeatures() throws IOException, SiftsException
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Failed to create AlignFrame");
+    SequenceI sq = af.getViewport().getAlignment().findName("FER2_ARATH");
+    assertNotNull(sq, "Didn't find FER2_ARATH");
+
+    /*
+     * need a Uniprot dbref for SIFTS mapping to work!!
+     */
+    sq.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
+
+    /*
+     * use local test PDB and SIFTS files
+     */
+    String pdbFilePath = new File(
+            "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+    PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
+    String siftsFilePath = new File(
+            "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
+            .getPath();
+    SiftsClient.setMockSiftsFile(new File(siftsFilePath));
+
+    StructureViewer structureViewer = new StructureViewer(af.getViewport()
+            .getStructureSelectionManager());
+    chimeraViewer = structureViewer.viewStructures(pdbEntry,
+            new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+
+    JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
+            .getBinding();
+    do
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
+      {
+      }
+    } while (!binding.isFinishedInit());
+
+    assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+
+    assertEquals(binding.getPdbCount(), 1);
+
+    /*
+     * check mapping is (sequence) 53-145 to (structure) 2-94 A/B
+     * (or possibly 52-145 to 1-94 - see JAL-2319)
+     */
+    StructureSelectionManager ssm = binding.getSsm();
+    String pdbFile = binding.getPdbFile()[0];
+    StructureMapping[] mappings = ssm.getMapping(pdbFile);
+    assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
+            "Failed to perform SIFTS mapping");
+    assertEquals(mappings.length, 2);
+    assertEquals(mappings[0].getChain(), "A");
+    assertEquals(mappings[0].getPDBResNum(53), 2);
+    assertEquals(mappings[0].getPDBResNum(145), 94);
+    assertEquals(mappings[1].getChain(), "B");
+    assertEquals(mappings[1].getPDBResNum(53), 2);
+    assertEquals(mappings[1].getPDBResNum(145), 94);
+
+    /*
+     * now add some features to FER2_ARATH 
+     */
+    // feature on a sequence region not mapped to structure:
+    sq.addSequenceFeature(new SequenceFeature("transit peptide",
+            "chloroplast", 1, 51, Float.NaN, null));
+    // feature on a region mapped to structure:
+    sq.addSequenceFeature(new SequenceFeature("domain",
+            "2Fe-2S ferredoxin-type", 55, 145, Float.NaN, null));
+    // on sparse positions of the sequence
+    sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
+            "Iron-Sulfur (2Fe-2S)", 91, 91, Float.NaN, null));
+    sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
+            "Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
+    // on a sequence region that is partially mapped to structure:
+    sq.addSequenceFeature(new SequenceFeature("helix", null, 50, 60,
+            Float.NaN, null));
+    // and again:
+    sq.addSequenceFeature(new SequenceFeature("chain", null, 50, 70,
+            Float.NaN, null));
+    // add numeric valued features - score is set as attribute value
+    sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
+            62, -2.1f, null));
+    sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 65,
+            65, 3.6f, null));
+    sq.addSequenceFeature(new SequenceFeature("RESNUM", "ALA:   2  4zhoA",
+            53, 53, Float.NaN, null));
+
+    /*
+     * set all features visible except for chain
+     */
+    af.setShowSeqFeatures(true);
+    FeatureRenderer fr = af.getFeatureRenderer();
+    fr.setVisible("transit peptide");
+    fr.setVisible("domain");
+    fr.setVisible("metal ion-binding site");
+    fr.setVisible("helix");
+    fr.setVisible("kd");
+    fr.setVisible("RESNUM");
+
+    /*
+     * 'perform' menu action to copy visible features to
+     * attributes in Chimera
+     */
+    // TODO rename and pull up method to binding interface
+    // once functionality is added for Jmol as well
+    binding.sendFeaturesToViewer(af.getViewport().getAlignPanel());
+
+    /*
+     * give Chimera time to open the commands file and execute it
+     */
+    try
+    {
+      Thread.sleep(1000);
+    } catch (InterruptedException e)
+    {
+    }
+
+    /*
+     * ask Chimera for its residue attribute names
+     */
+    List<String> reply = binding.sendChimeraCommand("list resattr", true);
+    // prefixed and sanitised attribute names for Jalview features:
+    assertTrue(reply.contains("resattr jv_domain"));
+    assertTrue(reply.contains("resattr jv_metal_ion_binding_site"));
+    assertTrue(reply.contains("resattr jv_helix"));
+    assertTrue(reply.contains("resattr jv_kd"));
+    assertTrue(reply.contains("resattr jv_RESNUM"));
+    // feature is not on a mapped region - no attribute created
+    assertFalse(reply.contains("resattr jv_transit_peptide"));
+    // feature is not visible - no attribute created
+    assertFalse(reply.contains("resattr jv_chain"));
+
+    /*
+     * ask Chimera for residues with an attribute
+     * 91 and 96 on sequence --> residues 40 and 45 on chains A and B
+     */
+    reply = binding.sendChimeraCommand(
+            "list resi att jv_metal_ion_binding_site", true);
+    assertEquals(reply.size(), 4);
+    assertTrue(reply
+            .contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+    assertTrue(reply
+            .contains("residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+    assertTrue(reply
+            .contains("residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+    assertTrue(reply
+            .contains("residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+
+    /*
+     * check attributes with score values
+     * sequence positions 62 and 65 --> residues 11 and 14 on chains A and B
+     */
+    reply = binding.sendChimeraCommand("list resi att jv_kd", true);
+    assertEquals(reply.size(), 4);
+    assertTrue(reply.contains("residue id #0:11.A jv_kd -2.1 index 11"));
+    assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
+    assertTrue(reply.contains("residue id #0:11.B jv_kd -2.1 index 11"));
+    assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
+
+    /*
+     * list residues with positive kd score 
+     */
+    reply = binding.sendChimeraCommand(
+            "list resi spec :*/jv_kd>0 attr jv_kd", true);
+    assertEquals(reply.size(), 2);
+    assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14"));
+    assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14"));
+
+    SiftsClient.setMockSiftsFile(null);
+    chimeraViewer.closeViewer(true);
+    chimeraViewer = null;
+  }
+
+  /**
+   * Test for creating Jalview features from attributes on mapped residues in
+   * Chimera. Note this uses local copies of PDB and SIFTS file, no network
+   * connection required.
+   * 
+   * @throws IOException
+   * @throws SiftsException
+   */
+  // External as this requires a local install of Chimera
+  @Test(groups = { "External" })
+  public void testGetAttributes() throws IOException, SiftsException
+  {
+    String inFile = "examples/uniref50.fa";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            DataSourceType.FILE);
+    assertNotNull(af, "Failed to create AlignFrame");
+    SequenceI fer2Arath = af.getViewport().getAlignment()
+            .findName("FER2_ARATH");
+    assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
+  
+    /*
+     * need a Uniprot dbref for SIFTS mapping to work!!
+     */
+    fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
+  
+    /*
+     * use local test PDB and SIFTS files
+     */
+    String pdbFilePath = new File(
+            "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+    PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
+    String siftsFilePath = new File(
+            "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
+            .getPath();
+    SiftsClient.setMockSiftsFile(new File(siftsFilePath));
+  
+    StructureViewer structureViewer = new StructureViewer(af.getViewport()
+            .getStructureSelectionManager());
+    chimeraViewer = structureViewer.viewStructures(pdbEntry,
+            new SequenceI[] { fer2Arath }, af.getCurrentView()
+                    .getAlignPanel());
+  
+    JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
+            .getBinding();
+    do
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
       {
-        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
-        {
-          final StructureViewer structureViewer = new StructureViewer(af
-                  .getViewport().getStructureSelectionManager());
-          structureViewer.setViewerType(ViewerType.CHIMERA);
-          JalviewStructureDisplayI chimeraViewer = structureViewer
-                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
-                          new SequenceI[] { sq }, af.getCurrentView()
-                                  .getAlignPanel());
-          /*
-           * Wait for viewer load thread to complete
-           */
-          while (!chimeraViewer.getBinding().isFinishedInit())
-          {
-            try
-            {
-              Thread.sleep(500);
-            } catch (InterruptedException e)
-            {
-            }
-          }
-          assertEquals(1, chimeraViewer.getBinding().getPdbCount());
-          chimeraViewer.closeViewer(true);
-          // todo: break here means only once through this loop?
-          break;
-        }
-        break;
       }
+    } while (!binding.isFinishedInit());
+  
+    assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera");
+  
+    assertEquals(binding.getPdbCount(), 1);
+  
+    /*
+     * 'perform' menu action to copy visible features to
+     * attributes in Chimera
+     */
+    // TODO rename and pull up method to binding interface
+    // once functionality is added for Jmol as well
+    binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
+            .getAlignPanel());
+
+    /*
+     * verify 22 residues have isHelix feature
+     * (may merge into ranges in future)
+     */
+    af.setShowSeqFeatures(true);
+    FeatureRenderer fr = af.getFeatureRenderer();
+    fr.setVisible("isHelix");
+    for (int res = 75; res <= 83; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
     }
+    for (int res = 117; res <= 123; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+    for (int res = 129; res <= 131; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+    for (int res = 143; res <= 145; res++)
+    {
+      checkFeaturesAtRes(fer2Arath, fr, res, "isHelix");
+    }
+
+    /*
+     * fetch a numeric valued attribute
+     */
+    binding.copyStructureAttributesToFeatures("phi", af.getViewport()
+            .getAlignPanel());
+    fr.setVisible("phi");
+    List<SequenceFeature> fs = fr.findFeaturesAtRes(fer2Arath, 54);
+    assertEquals(fs.size(), 3);
+    assertEquals(fs.get(0).getType(), "RESNUM");
+    assertEquals(fs.get(1).getType(), "phi");
+    assertEquals(fs.get(2).getType(), "phi");
+    assertEquals(fs.get(1).getDescription(), "A"); // chain
+    assertEquals(fs.get(2).getDescription(), "B");
+    assertEquals(fs.get(1).getScore(), -131.0713f, 0.001f);
+    assertEquals(fs.get(2).getScore(), -127.39512, 0.001f);
+
+    /*
+     * tear down - also in AfterMethod
+     */
+    SiftsClient.setMockSiftsFile(null);
+    chimeraViewer.closeViewer(true);
+    chimeraViewer = null;
+  }
+
+  /**
+   * Helper method to verify new feature at a sequence position
+   * 
+   * @param seq
+   * @param fr
+   * @param res
+   * @param featureType
+   */
+  protected void checkFeaturesAtRes(SequenceI seq, FeatureRenderer fr,
+          int res, String featureType)
+  {
+    String where = "at position " + res;
+    List<SequenceFeature> fs = fr.findFeaturesAtRes(seq, res);
+    assertEquals(fs.size(), 2, where);
+    assertEquals(fs.get(0).getType(), "RESNUM", where);
+    SequenceFeature sf = fs.get(1);
+    assertEquals(sf.getType(), featureType, where);
+    assertEquals(sf.getFeatureGroup(), "Chimera", where);
+    assertEquals(sf.getDescription(), "True", where);
+    assertEquals(sf.getScore(), Float.NaN, where);
   }
 }
diff --git a/test/jalview/ext/rbvi/chimera/testProps.jvprops b/test/jalview/ext/rbvi/chimera/testProps.jvprops
index 95da22e..5c08d8e 100644
--- a/test/jalview/ext/rbvi/chimera/testProps.jvprops
+++ b/test/jalview/ext/rbvi/chimera/testProps.jvprops
@@ -1,85 +1,82 @@
-#---JalviewX Properties File---
-#Fri Apr 25 09:54:25 BST 2014
-SCREEN_Y=768
-SCREEN_X=936
-SHOW_WSDISCOVERY_ERRORS=true
-LATEST_VERSION=2.8.0b1
-SHOW_CONSERVATION=true
+ANNOTATIONCOLOUR_MAX=ff0000
+ANNOTATIONCOLOUR_MIN=ffc800
+ANTI_ALIAS=false
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+AUTO_CALC_CONSENSUS=true
+BLC_JVSUFFIX=true
+BUILD_DATE=01 November 2013
+CLUSTAL_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+DAS_LOCAL_SOURCE=
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+DEFAULT_COLOUR=None
+DEFAULT_FILE_FORMAT=FASTA
+FASTA_JVSUFFIX=true
+FIGURE_AUTOIDWIDTH=false
+FIGURE_USERIDWIDTH=
+FONT_NAME=SansSerif
+FONT_SIZE=10
+FONT_STYLE=plain
+GAP_SYMBOL=-
+ID_ITALICS=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
 JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+JAVA_CONSOLE_SCREEN_HEIGHT=162
 JAVA_CONSOLE_SCREEN_WIDTH=450
+JAVA_CONSOLE_SCREEN_X=830
+JAVA_CONSOLE_SCREEN_Y=475
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
 LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
-ID_ITALICS=true
-SORT_ALIGNMENT=No sort
-SHOW_IDENTITY=true
-WSMENU_BYHOST=false
-SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
-SHOW_FULLSCREEN=false
-RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
-FONT_NAME=SansSerif
-BLC_JVSUFFIX=true
-VERSION_CHECK=false
-YEAR=2011
-SHOW_DBREFS_TOOLTIP=true
+LATEST_VERSION=2.8.0b1
 MSF_JVSUFFIX=true
-SCREENGEOMETRY_HEIGHT=1600
-JAVA_CONSOLE_SCREEN_Y=475
-JAVA_CONSOLE_SCREEN_X=830
+NOQUESTIONNAIRES=true
+PAD_GAPS=false
 PFAM_JVSUFFIX=true
+PILEUP_JVSUFFIX=true
 PIR_JVSUFFIX=true
-STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
-JAVA_CONSOLE_SCREEN_HEIGHT=162
 PIR_MODELLER=false
-GAP_SYMBOL=-
-SHOW_QUALITY=true
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+RIGHT_ALIGN_IDS=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+SCREEN_HEIGHT=650
+SCREEN_WIDTH=900
+SCREEN_X=936
+SCREEN_Y=768
+SCREENGEOMETRY_HEIGHT=1600
+SCREENGEOMETRY_WIDTH=2560
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_ANNOTATIONS=true
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_CONSENSUS_LOGO=false
+SHOW_CONSERVATION=true
+SHOW_DBREFS_TOOLTIP=true
+SHOW_ENFIN_SERVICES=true
+SHOW_FULLSCREEN=false
+SHOW_GROUP_CONSENSUS=false
 SHOW_GROUP_CONSERVATION=false
+SHOW_IDENTITY=true
+SHOW_JAVA_CONSOLE=false
+SHOW_JVSUFFIX=true
 SHOW_JWS2_SERVICES=true
 SHOW_NPFEATS_TOOLTIP=true
-FONT_STYLE=plain
-ANTI_ALIAS=false
-SORT_BY_TREE=false
-RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
-AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
-JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
-SHOW_GROUP_CONSENSUS=false
-SHOW_CONSENSUS_HISTOGRAM=true
 SHOW_OVERVIEW=false
-AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
-FIGURE_AUTOIDWIDTH=false
-SCREEN_WIDTH=900
-ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_QUALITY=true
 SHOW_STARTUP_FILE=false
-RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
-DEFAULT_FILE_FORMAT=FASTA
-SHOW_JAVA_CONSOLE=false
-VERSION=2.8b1
-FIGURE_USERIDWIDTH=
-WSMENU_BYTYPE=false
-DEFAULT_COLOUR=None
-NOQUESTIONNAIRES=true
-JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
-BUILD_DATE=01 November 2013
-PILEUP_JVSUFFIX=true
-SHOW_CONSENSUS_LOGO=false
-SCREENGEOMETRY_WIDTH=2560
-SHOW_ANNOTATIONS=true
-JALVIEW_RSS_WINDOW_SCREEN_Y=0
-USAGESTATS=false
-JALVIEW_RSS_WINDOW_SCREEN_X=0
 SHOW_UNCONSERVED=false
-SHOW_JVSUFFIX=true
-DAS_LOCAL_SOURCE=
-SCREEN_HEIGHT=650
-ANNOTATIONCOLOUR_MAX=ff0000
-AUTO_CALC_CONSENSUS=true
-FASTA_JVSUFFIX=true
-DAS_ACTIVE_SOURCE=uniprot\t
-JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
-PAD_GAPS=false
-CLUSTAL_JVSUFFIX=true
-SHOW_ENFIN_SERVICES=true
-FONT_SIZE=10
-RIGHT_ALIGN_IDS=false
+SHOW_WSDISCOVERY_ERRORS=true
+SORT_ALIGNMENT=No sort
+SORT_BY_TREE=false
+STARTUP_FILE=
+USAGESTATS=false
 USE_PROXY=false
+VERSION_CHECK=false
+VERSION=2.8b1
 WRAP_ALIGNMENT=false
-#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
-DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+WSMENU_BYHOST=false
+WSMENU_BYTYPE=false
+YEAR=2011
diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
new file mode 100644
index 0000000..b228ba1
--- /dev/null
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -0,0 +1,221 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.viewmodel.ViewportRanges;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class AlignmentPanelTest
+{
+  SequenceI seq1 = new Sequence(
+          "Seq1",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq2 = new Sequence(
+          "Seq2",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq3 = new Sequence(
+          "Seq3",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq4 = new Sequence(
+          "Seq4",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq5 = new Sequence(
+          "Seq5",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq6 = new Sequence(
+          "Seq6",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq7 = new Sequence(
+          "Seq7",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq8 = new Sequence(
+          "Seq8",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq9 = new Sequence(
+          "Seq9",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq10 = new Sequence(
+          "Seq10",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq11 = new Sequence(
+          "Seq11",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq12 = new Sequence(
+          "Seq12",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq13 = new Sequence(
+          "Seq13",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq14 = new Sequence(
+          "Seq14",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq15 = new Sequence(
+          "Seq15",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq16 = new Sequence(
+          "Seq16",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq17 = new Sequence(
+          "Seq17",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq18 = new Sequence(
+          "Seq18",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq19 = new Sequence(
+          "Seq19",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq20 = new Sequence(
+          "Seq20",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq21 = new Sequence(
+          "Seq21",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq22 = new Sequence(
+          "Seq22",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  SequenceI seq23 = new Sequence(
+          "Seq23",
+          "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+  AlignFrame af;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Jalview.main(new String[] { "-nonews", "-props",
+        "test/jalview/testProps.jvprops" });
+
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+
+    /*
+     * wait for Consensus thread to complete
+     */
+    synchronized (this)
+    {
+      while (af.getViewport().getConsensusSeq() == null)
+      {
+        try
+        {
+          wait(50);
+        } catch (InterruptedException e)
+        {
+        }
+      }
+    }
+  }
+
+
+  /**
+   * Test side effect that end residue is set correctly by setScrollValues, with
+   * or without hidden columns
+   */
+  @Test(groups = "Functional")
+  public void TestSetScrollValues()
+  {
+    ViewportRanges ranges = af.getViewport().getRanges();
+    af.alignPanel.setScrollValues(0, 0);
+
+    int oldres = ranges.getEndRes();
+    af.alignPanel.setScrollValues(-1, 5);
+
+    // setting -ve x value does not change residue
+    assertEquals(ranges.getEndRes(), oldres);
+
+    af.alignPanel.setScrollValues(0, 5);
+
+    // setting 0 as x value does not change residue
+    assertEquals(ranges.getEndRes(), oldres);
+
+    af.alignPanel.setScrollValues(5, 5);
+    // setting x value to 5 extends endRes by 5 residues
+    assertEquals(ranges.getEndRes(), oldres + 5);
+
+    // scroll to position after hidden columns sets endres to oldres (width) +
+    // position
+    int scrollpos = 60;
+    af.getViewport().hideColumns(30, 50);
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(ranges.getEndRes(), oldres + scrollpos);
+
+    // scroll to position within hidden columns, still sets endres to oldres +
+    // position
+    // not sure if this is actually correct behaviour but this is what Jalview
+    // currently does
+    scrollpos = 40;
+    af.getViewport().showAllHiddenColumns();
+    af.getViewport().hideColumns(30, 50);
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(ranges.getEndRes(), oldres + scrollpos);
+
+    // scroll to position within <width> distance of the end of the alignment
+    // endRes should be set to width of alignment - 1
+    scrollpos = 130;
+    af.getViewport().showAllHiddenColumns();
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(ranges.getEndRes(), af.getViewport()
+            .getAlignment().getWidth() - 1);
+
+    // now hide some columns, and scroll to position within <width>
+    // distance of the end of the alignment
+    // endRes should be set to width of alignment - 1 - the number of hidden
+    // columns
+    af.getViewport().hideColumns(30, 50);
+    af.alignPanel.setScrollValues(scrollpos, 5);
+    assertEquals(ranges.getEndRes(), af.getViewport()
+            .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
+                                                  // columns
+  }
+}
diff --git a/test/jalview/gui/AnnotationChooserTest.java b/test/jalview/gui/AnnotationChooserTest.java
index 38c1855..fbdda09 100644
--- a/test/jalview/gui/AnnotationChooserTest.java
+++ b/test/jalview/gui/AnnotationChooserTest.java
@@ -326,7 +326,7 @@ public class AnnotationChooserTest
 
     types = AnnotationChooser.getAnnotationTypes(
             parentPanel.getAlignment(), false);
-    assertEquals("Not six annotation types", 6, types.size());
+    assertEquals("Not six annotation types", 7, types.size());
     assertTrue("IUPRED missing", types.contains("IUPRED"));
     assertTrue("JMol missing", types.contains("JMol"));
     assertTrue("Beauty missing", types.contains("Beauty"));
@@ -334,6 +334,7 @@ public class AnnotationChooserTest
     assertTrue("Consensus missing", types.contains("Consensus"));
     assertTrue("Quality missing", types.contains("Quality"));
     assertTrue("Conservation missing", types.contains("Conservation"));
+    assertTrue("Occupancy missing", types.contains("Occupancy"));
   }
 
   /**
@@ -357,18 +358,20 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     setSelected(getTypeCheckbox("JMol"), true);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertFalse(anns[5].visible); // JMol for seq3 - not selected but hidden
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1 - selected and hidden
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertFalse(anns[6].visible); // JMol for seq3 - not selected but hidden
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1 - selected and hidden
   }
 
   /**
@@ -395,17 +398,19 @@ public class AnnotationChooserTest
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
 
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     setSelected(getTypeCheckbox("JMol"), true);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3 not in selection group
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1 in selection group
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3 not in selection group
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1 in selection group
   }
 
   /**
@@ -435,19 +440,35 @@ public class AnnotationChooserTest
 
     // select JMol - all hidden
     setSelected(typeCheckbox, true);
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+    assertFalse(anns[autocalc + 4].visible); // JMol for seq1
 
     // deselect JMol - all unhidden
     setSelected(typeCheckbox, false);
-    assertTrue(anns[0].visible); // Conservation
-    assertTrue(anns[1].visible); // Quality
-    assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertTrue(anns[7].visible); // JMol for seq1
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
+  }
+
+  /**
+   * Returns a count of autocalculated annotations in the set provided
+   * 
+   * @param anns
+   * @return
+   */
+  private int countAutocalc(AlignmentAnnotation[] anns)
+  {
+    int count = 0;
+    for (AlignmentAnnotation ann : anns)
+    {
+      if (ann.autoCalculated)
+      {
+        count++;
+      }
+    }
+    return count;
   }
 
   /**
@@ -510,18 +531,15 @@ public class AnnotationChooserTest
     setSelected(allSequencesCheckbox, true);
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+    assertFalse(anns[autocalc + 4].visible); // JMol for seq1
     // ...now show them...
     setSelected(showCheckbox, true);
-    assertTrue(anns[0].visible); // Conservation
-    assertTrue(anns[1].visible); // Quality
-    assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertTrue(anns[7].visible); // JMol for seq1
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
   }
 
   /**
@@ -551,19 +569,16 @@ public class AnnotationChooserTest
     setSelected(hideCheckbox, true);
     setSelected(getTypeCheckbox("JMol"), true);
 
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertFalse(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertFalse(anns[autocalc + 4].visible); // JMol for seq1
     // ...now show them...
     setSelected(showCheckbox, true);
 
-    assertTrue(anns[0].visible); // Conservation
-    assertTrue(anns[1].visible); // Quality
-    assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertTrue(anns[7].visible); // JMol for seq1
+    for (AlignmentAnnotation ann : anns)
+    {
+      assertTrue(ann.visible);
+    }
   }
 
   /**
@@ -592,19 +607,21 @@ public class AnnotationChooserTest
     final Checkbox typeCheckbox = getTypeCheckbox("JMol");
     // select JMol - all shown
     setSelected(typeCheckbox, true);
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     // deselect JMol - all hidden
     setSelected(typeCheckbox, false);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertFalse(anns[5].visible); // JMol for seq3
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertFalse(anns[6].visible); // JMol for seq3
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1
   }
 
   /**
@@ -633,19 +650,21 @@ public class AnnotationChooserTest
 
     // select JMol - should remain visible
     setSelected(getTypeCheckbox("JMol"), true);
-    assertTrue(anns[5].visible); // JMol for seq3
-    assertTrue(anns[7].visible); // JMol for seq1
+    int autocalc = countAutocalc(anns);
+    assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+    assertTrue(anns[autocalc + 4].visible); // JMol for seq1
 
     // deselect JMol - should be hidden for selected sequences only
     setSelected(getTypeCheckbox("JMol"), false);
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertTrue(anns[3].visible); // IUPred for seq0
-    assertTrue(anns[4].visible); // Beauty
-    assertTrue(anns[5].visible); // JMol for seq3 not in selection group
-    assertTrue(anns[6].visible); // IUPRED for seq2
-    assertFalse(anns[7].visible); // JMol for seq1 in selection group
+    assertTrue(anns[3].visible); // Occupancy
+    assertTrue(anns[4].visible); // IUPred for seq0
+    assertTrue(anns[5].visible); // Beauty
+    assertTrue(anns[6].visible); // JMol for seq3 not in selection group
+    assertTrue(anns[7].visible); // IUPRED for seq2
+    assertFalse(anns[8].visible); // JMol for seq1 in selection group
   }
 
   /**
@@ -721,12 +740,12 @@ public class AnnotationChooserTest
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
-    // remember 3 annotations to skip (Conservation/Quality/Consensus)
-    assertFalse(testee.isInActionScope(anns[3]));
-    assertFalse(testee.isInActionScope(anns[4]));
-    assertFalse(testee.isInActionScope(anns[5]));
-    assertTrue(testee.isInActionScope(anns[6]));
-    assertTrue(testee.isInActionScope(anns[7]));
+    int autocalc = countAutocalc(anns);
+    assertFalse(testee.isInActionScope(anns[autocalc]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 1]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 2]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 3]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 4]));
   }
 
   /**
@@ -747,12 +766,12 @@ public class AnnotationChooserTest
 
     AlignmentAnnotation[] anns = parentPanel.getAlignment()
             .getAlignmentAnnotation();
-    // remember 3 annotations to skip (Conservation/Quality/Consensus)
-    assertTrue(testee.isInActionScope(anns[3]));
-    assertTrue(testee.isInActionScope(anns[4]));
-    assertTrue(testee.isInActionScope(anns[5]));
-    assertFalse(testee.isInActionScope(anns[6]));
-    assertFalse(testee.isInActionScope(anns[7]));
+    int autocalc = countAutocalc(anns);
+    assertTrue(testee.isInActionScope(anns[autocalc]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 1]));
+    assertTrue(testee.isInActionScope(anns[autocalc + 2]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 3]));
+    assertFalse(testee.isInActionScope(anns[autocalc + 4]));
   }
 
   /**
@@ -787,11 +806,12 @@ public class AnnotationChooserTest
     assertTrue(anns[0].visible); // Conservation
     assertTrue(anns[1].visible); // Quality
     assertTrue(anns[2].visible); // Consensus
-    assertFalse(anns[3].visible); // IUPRED
-    assertTrue(anns[4].visible); // Beauty (not seq-related)
-    assertFalse(anns[5].visible); // JMol
-    assertFalse(anns[6].visible); // IUPRED
-    assertFalse(anns[7].visible); // JMol
+    assertTrue(anns[3].visible); // Occupancy
+    assertFalse(anns[4].visible); // IUPRED
+    assertTrue(anns[5].visible); // Beauty (not seq-related)
+    assertFalse(anns[6].visible); // JMol
+    assertFalse(anns[7].visible); // IUPRED
+    assertFalse(anns[8].visible); // JMol
 
     // reset - should all be visible
     testee.resetOriginalState();
diff --git a/test/jalview/gui/AnnotationRowFilterTest.java b/test/jalview/gui/AnnotationRowFilterTest.java
new file mode 100644
index 0000000..69a41c5
--- /dev/null
+++ b/test/jalview/gui/AnnotationRowFilterTest.java
@@ -0,0 +1,121 @@
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import java.util.Vector;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+/**
+ * Tests for methods of base class of annotation column or colour chooser
+ */
+public class AnnotationRowFilterTest
+{
+  AlignFrame af;
+
+  private AnnotationRowFilter testee;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty(
+            Preferences.SHOW_AUTOCALC_ABOVE, Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+    testee = new AnnotationRowFilter(af.viewport, af.alignPanel)
+    {
+      @Override
+      public void valueChanged(boolean updateAllAnnotation)
+      {
+      }
+
+      @Override
+      public void updateView()
+      {
+      }
+
+      @Override
+      public void reset()
+      {
+      }
+    };
+  }
+
+  /**
+   * Test the method that builds the drop-down list of annotations to choose
+   * from for colour by annotation or select columns by annotation
+   */
+  @Test(groups = "Functional")
+  public void testGetAnnotationItems()
+  {
+    AlignmentI al = af.getViewport().getAlignment();
+    SequenceI seq1 = al.findSequenceMatch("FER_CAPAA")[0];
+    SequenceI seq2 = al.findSequenceMatch("FER_BRANA")[0];
+
+    AlignmentAnnotation ann1 = new AlignmentAnnotation("ann1Label", "ann1",
+            null);
+    al.addAnnotation(ann1);
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("Significance",
+            "ann2", null);
+    al.addAnnotation(ann2);
+    /*
+     * a second Significance alignment annotation
+     */
+    AlignmentAnnotation ann2a = new AlignmentAnnotation("Significance",
+            "ann2", null);
+    al.addAnnotation(ann2a);
+
+    AlignmentAnnotation ann3 = new AlignmentAnnotation("Jronn", "Jronn",
+            null);
+    ann3.setSequenceRef(seq1);
+    al.addAnnotation(ann3);
+    AlignmentAnnotation ann4 = new AlignmentAnnotation("Jronn", "Jronn",
+            null);
+    ann4.setSequenceRef(seq2);
+    al.addAnnotation(ann4);
+    AlignmentAnnotation ann5 = new AlignmentAnnotation("Jnet", "Jnet", null);
+    ann5.setSequenceRef(seq2);
+    al.addAnnotation(ann5);
+    /*
+     * a second Jnet annotation for FER_BRANA
+     */
+    AlignmentAnnotation ann6 = new AlignmentAnnotation("Jnet", "Jnet", null);
+    ann6.setSequenceRef(seq2);
+    al.addAnnotation(ann6);
+
+    /*
+     * drop-down items with 'Per-sequence only' not checked
+     */
+    Vector<String> items = testee.getAnnotationItems(false);
+    assertEquals(
+            items.toString(),
+            "[Conservation, Quality, Consensus, Occupancy, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]");
+    assertEquals(testee.getAnnotationMenuLabel(ann1), "ann1Label");
+    assertEquals(testee.getAnnotationMenuLabel(ann2), "Significance");
+    assertEquals(testee.getAnnotationMenuLabel(ann2a), "Significance_1");
+    assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn_FER_CAPAA");
+    assertEquals(testee.getAnnotationMenuLabel(ann4), "Jronn_FER_BRANA");
+    assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet_FER_BRANA");
+    assertEquals(testee.getAnnotationMenuLabel(ann6), "Jnet_FER_BRANA_2");
+
+    /*
+     * drop-down items with 'Per-sequence only' checked
+     */
+    items = testee.getAnnotationItems(true);
+    assertEquals(items.toString(), "[Jronn, Jnet]");
+    // the first annotation of the type is associated with the menu item
+    assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn");
+    assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet");
+  }
+}
diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java
index 81289b0..29a9a52 100644
--- a/test/jalview/gui/SequenceRendererTest.java
+++ b/test/jalview/gui/SequenceRendererTest.java
@@ -53,10 +53,10 @@ public class SequenceRendererTest
     av.setGlobalColourScheme(new ZappoColourScheme());
 
     // @see ResidueProperties.zappo
-    assertEquals(Color.pink, sr.getResidueColour(seq, 0, null)); // M
-    assertEquals(Color.green, sr.getResidueColour(seq, 2, null)); // T
-    assertEquals(Color.magenta, sr.getResidueColour(seq, 5, null)); // G
-    assertEquals(Color.orange, sr.getResidueColour(seq, 12, null)); // F
+    assertEquals(Color.pink, sr.getResidueBoxColour(seq, 0)); // M
+    assertEquals(Color.green, sr.getResidueBoxColour(seq, 2)); // T
+    assertEquals(Color.magenta, sr.getResidueBoxColour(seq, 5)); // G
+    assertEquals(Color.orange, sr.getResidueBoxColour(seq, 12)); // F
   }
   // TODO more tests for getResidueBoxColour covering groups, feature rendering,
   // gaps, overview...
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
new file mode 100644
index 0000000..59566ed
--- /dev/null
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -0,0 +1,448 @@
+package jalview.renderer.seqfeatures;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertTrue;
+
+import jalview.api.FeatureColourI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.FeatureRenderer;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.schemes.FeatureColour;
+
+import java.awt.Color;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for feature colour determination, including but not limited to
+ * <ul>
+ * <li>gap position</li>
+ * <li>no features present</li>
+ * <li>features present but show features turned off</li>
+ * <li>features displayed but selected feature turned off</li>
+ * <li>features displayed but feature group turned off</li>
+ * <li>feature displayed but none at the specified position</li>
+ * <li>multiple features at position, with no transparency</li>
+ * <li>multiple features at position, with transparency</li>
+ * <li>score graduated feature colour</li>
+ * <li>contact feature start at the selected position</li>
+ * <li>contact feature end at the selected position</li>
+ * <li>contact feature straddling the selected position (not shown)</li>
+ * </ul>
+ */
+public class FeatureColourFinderTest
+{
+  private AlignViewport av;
+
+  private SequenceI seq;
+
+  private FeatureColourFinder finder;
+
+  private AlignFrame af;
+
+  private FeatureRenderer fr;
+
+  @BeforeTest(alwaysRun = true)
+  public void setUp()
+  {
+    // aligned column 8 is sequence position 6
+    String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
+    af = new FileLoader().LoadFileWaitTillLoaded(s,
+            DataSourceType.PASTE);
+    av = af.getViewport();
+    seq = av.getAlignment().getSequenceAt(0);
+    fr = af.getFeatureRenderer();
+    finder = new FeatureColourFinder(fr);
+  }
+
+  /**
+   * Clear down any sequence features before each test (not as easy as it
+   * sounds...)
+   */
+  @BeforeMethod(alwaysRun = true)
+  public void setUpBeforeTest()
+  {
+    SequenceFeature[] sfs = seq.getSequenceFeatures();
+    if (sfs != null)
+    {
+      for (SequenceFeature sf : sfs)
+      {
+        seq.deleteFeature(sf);
+      }
+    }
+    fr.findAllFeatures(true);
+
+    /*
+     * reset all feature groups to visible
+     */
+    for (String group : fr.getGroups(false))
+    {
+      fr.setGroupVisibility(group, true);
+    }
+
+    fr.clearRenderOrder();
+    av.setShowSequenceFeatures(true);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_noFeatures()
+  {
+    av.setShowSequenceFeatures(false);
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.blue);
+
+    av.setShowSequenceFeatures(true);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.blue);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_noFeaturesShown()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(false);
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.blue);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_singleFeatureAtPosition()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    fr.setColour("Metal", new FeatureColour(Color.red));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.red);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_gapPosition()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
+            null));
+    fr.setColour("Metal", new FeatureColour(Color.red));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+    Color c = finder.findFeatureColour(null, seq, 6);
+    assertEquals(c, Color.white);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_multipleFeaturesAtPositionNoTransparency()
+  {
+    /*
+     * featuresAdded -> FeatureRendererModel.updateRenderOrder which adds any
+     * new features 'on top' (but reverses the order of any added features)
+     */
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
+            Float.NaN, "DomainGroup"));
+    FeatureColour green = new FeatureColour(Color.green);
+    fr.setColour("Domain", green);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+
+    /*
+     * expect Domain (green) to be rendered above Metal (red)
+     */
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.green);
+
+    /*
+     * now promote Metal above Domain
+     * - currently no way other than mimicking reordering of
+     * table in Feature Settings
+     */
+    Object[][] data = new Object[2][];
+    data[0] = new Object[] { "Metal", red, true };
+    data[1] = new Object[] { "Domain", green, true };
+    fr.setFeaturePriority(data);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.red);
+
+    /*
+     * ..and turn off display of Metal
+     */
+    data[0][2] = false;
+    fr.setFeaturePriority(data);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.green);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_singleFeatureNotAtPosition()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 8, 12,
+            Float.NaN, "MetalGroup"));
+    fr.setColour("Metal", new FeatureColour(Color.red));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+    // column 2 = sequence position 3
+    Color c = finder.findFeatureColour(Color.blue, seq, 2);
+    assertEquals(c, Color.blue);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_featureTypeNotDisplayed()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.red);
+
+    /*
+     * turn off display of Metal - is this the easiest way to do it??
+     */
+    Object[][] data = new Object[1][];
+    data[0] = new Object[] { "Metal", red, false };
+    fr.setFeaturePriority(data);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.blue);
+
+    /*
+     * turn display of Metal back on
+     */
+    data[0] = new Object[] { "Metal", red, true };
+    fr.setFeaturePriority(data);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.red);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_featureGroupNotDisplayed()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.red);
+
+    /*
+     * turn off display of MetalGroup
+     */
+    fr.setGroupVisibility("MetalGroup", false);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.blue);
+
+    /*
+     * turn display of MetalGroup back on
+     */
+    fr.setGroupVisibility("MetalGroup", true);
+    c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.red);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_contactFeature()
+  {
+    /*
+     * currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
+     */
+    seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
+            "Contact", 2, 12, Float.NaN, "Disulphide"));
+    fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+
+    /*
+     * Contact positions are residues 2 and 12
+     * which are columns 1 and 14
+     * positions in between don't count for a contact feature!
+     */
+    Color c = finder.findFeatureColour(Color.blue, seq, 10);
+    assertEquals(c, Color.blue);
+    c = finder.findFeatureColour(Color.blue, seq, 8);
+    assertEquals(c, Color.blue);
+    c = finder.findFeatureColour(Color.blue, seq, 1);
+    assertEquals(c, Color.red);
+    c = finder.findFeatureColour(Color.blue, seq, 14);
+    assertEquals(c, Color.red);
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_graduatedFeatureColour()
+  {
+    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
+            2, 0f, "KdGroup"));
+    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
+            4, 5f, "KdGroup"));
+    seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
+            7, 10f, "KdGroup"));
+
+    /*
+     * graduated colour from 0 to 10
+     */
+    Color min = new Color(100, 50, 150);
+    Color max = new Color(200, 0, 100);
+    FeatureColourI fc = new FeatureColour(min, max, 0, 10);
+    fr.setColour("kd", fc);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+
+    /*
+     * position 2, column 1, score 0 - minimum colour in range
+     */
+    Color c = finder.findFeatureColour(Color.blue, seq, 1);
+    assertEquals(c, min);
+
+    /*
+     * position 7, column 9, score 10 - maximum colour in range
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 9);
+    assertEquals(c, max);
+
+    /*
+     * position 4, column 3, score 5 - half way from min to max
+     */
+    c = finder.findFeatureColour(Color.blue, seq, 3);
+    assertEquals(c, new Color(150, 25, 125));
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_transparencySingleFeature()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+  
+    /*
+     * the FeatureSettings transparency slider has range 0-70 which
+     * corresponds to a transparency value of 1 - 0.3
+     * A value of 0.4 gives a combination of
+     * 0.4 * red(255, 0, 0) + 0.6 * cyan(0, 255, 255) = (102, 153, 153)
+     */
+    fr.setTransparency(0.4f);
+    Color c = finder.findFeatureColour(Color.cyan, seq, 10);
+    assertEquals(c, new Color(102, 153, 153));
+  }
+
+  @Test(groups = "Functional")
+  public void testFindFeatureColour_transparencyTwoFeatures()
+  {
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    seq.addSequenceFeature(new SequenceFeature("Domain", "Domain", 4, 15,
+            Float.NaN, "DomainGroup"));
+    FeatureColour green = new FeatureColour(Color.green);
+    fr.setColour("Domain", green);
+    fr.featuresAdded();
+    av.setShowSequenceFeatures(true);
+  
+    /*
+     * Domain (green) rendered above Metal (red) above background (cyan)
+     * 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
+     * 2) 0.6* green(0, 255, 0) + 0.4 * (153, 102, 102) = (61, 194, 41) rounded
+     */
+    fr.setTransparency(0.6f);
+    Color c = finder.findFeatureColour(Color.cyan, seq, 10);
+    assertEquals(c, new Color(61, 194, 41));
+  
+    /*
+     * now promote Metal above Domain
+     * - currently no way other than mimicking reordering of
+     * table in Feature Settings
+     * Metal (red) rendered above Domain (green) above background (cyan)
+     * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
+     * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
+     */
+    Object[][] data = new Object[2][];
+    data[0] = new Object[] { "Metal", red, true };
+    data[1] = new Object[] { "Domain", green, true };
+    fr.setFeaturePriority(data);
+    c = finder.findFeatureColour(Color.cyan, seq, 10);
+    assertEquals(c, new Color(153, 102, 41));
+  
+    /*
+     * ..and turn off display of Metal
+     * Domain (green) above background (pink)
+     * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
+     */
+    data[0][2] = false;
+    fr.setFeaturePriority(data);
+    c = finder.findFeatureColour(Color.pink, seq, 10);
+    assertEquals(c, new Color(102, 223, 70));
+  }
+
+  @Test(groups = "Functional")
+  public void testNoFeaturesDisplayed()
+  {
+    /*
+     * no features on alignment to render
+     */
+    assertTrue(finder.noFeaturesDisplayed());
+
+    /*
+     * add a feature
+     * it will be automatically set visible but we leave
+     * the viewport configured not to show features
+     */
+    av.setShowSequenceFeatures(false);
+    seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12,
+            Float.NaN, "MetalGroup"));
+    FeatureColour red = new FeatureColour(Color.red);
+    fr.setColour("Metal", red);
+    fr.featuresAdded();
+    assertTrue(finder.noFeaturesDisplayed());
+
+    /*
+     * turn on feature display
+     */
+    av.setShowSequenceFeatures(true);
+    assertFalse(finder.noFeaturesDisplayed());
+
+    /*
+     * turn off display of Metal
+     */
+    Object[][] data = new Object[1][];
+    data[0] = new Object[] { "Metal", red, false };
+    fr.setFeaturePriority(data);
+    assertTrue(finder.noFeaturesDisplayed());
+
+    /*
+     * turn display of Metal back on
+     */
+    fr.setVisible("Metal");
+    assertFalse(finder.noFeaturesDisplayed());
+
+    /*
+     * turn off MetalGroup - has no effect here since the group of a
+     * sequence feature instance is independent of its type
+     */
+    fr.setGroupVisibility("MetalGroup", false);
+    assertFalse(finder.noFeaturesDisplayed());
+
+    /*
+     * a finder with no feature renderer
+     */
+    FeatureColourFinder finder2 = new FeatureColourFinder(null);
+    assertTrue(finder2.noFeaturesDisplayed());
+  }
+}
diff --git a/test/jalview/schemes/AnnotationColourGradientTest.java b/test/jalview/schemes/AnnotationColourGradientTest.java
new file mode 100644
index 0000000..1c93856
--- /dev/null
+++ b/test/jalview/schemes/AnnotationColourGradientTest.java
@@ -0,0 +1,300 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class AnnotationColourGradientTest
+{
+  final static int WIDTH = 11;
+
+  final static int THRESHOLD_FIVE = 5;
+
+  private AlignmentAnnotation ann;
+
+  private SequenceI seq;
+
+  private AlignmentI al;
+
+  Color minColour = new Color(50, 200, 150);
+
+  Color maxColour = new Color(150, 100, 250);
+
+  /**
+   * Setup creates an annotation over 11 columns with values 0-10 and threshold
+   * 5
+   */
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Annotation[] anns = new Annotation[WIDTH];
+    /*
+     * set annotations with values 0-10, graded colours
+     */
+    for (int col = 0; col < WIDTH; col++)
+    {
+      int hue = col * 20;
+      Color colour = new Color(hue, hue, hue);
+      anns[col] = new Annotation("a", "a", 'a', col, colour);
+    }
+
+    seq = new Sequence("", "");
+    al = new Alignment(new SequenceI[]{ seq});
+    
+    /*
+     * AlignmentAnnotation constructor works out min-max range
+     */
+    ann = new AlignmentAnnotation("", "", anns);
+    ann.setThreshold(new GraphLine(THRESHOLD_FIVE, "", Color.RED));
+    seq.addAlignmentAnnotation(ann);
+  }
+
+  @Test(groups = "Functional")
+  public void testShadeCalculation_noThreshold()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
+    for (int col = 0; col < WIDTH; col++)
+    {
+      Color result = testee.shadeCalculation(ann, col);
+      /*
+       * column <n> is n/10 of the way from minCol to maxCol
+       */
+      Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+              150 + 10 * col);
+      assertEquals(result, expected, "for column " + col);
+    }
+  }
+
+  /**
+   * Test the 'colour above threshold' case
+   */
+  @Test(groups = "Functional")
+  public void testShadeCalculation_aboveThreshold()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
+    for (int col = 0; col < WIDTH; col++)
+    {
+      Color result = testee.shadeCalculation(ann, col);
+      /*
+       * colour is derived regardless of the threshold value 
+       * (the renderer will suppress colouring if above/below threshold)
+       */
+      Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+              150 + 10 * col);
+      assertEquals(result, expected, "for column " + col);
+    }
+
+    /*
+     * now make 6-10 the span of the colour range
+     * (annotation value == column number in this test)
+     */
+    testee.setThresholdIsMinMax(true);
+    for (int col = 0; col < THRESHOLD_FIVE; col++)
+    {
+      /*
+       * colours below the threshold are computed as before
+       */
+      Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+              150 + 10 * col);
+      Color result = testee.shadeCalculation(ann, col);
+      assertEquals(result, expected, "for column " + col);
+    }
+    for (int col = THRESHOLD_FIVE; col < WIDTH; col++)
+    {
+      /*
+       * colours for values >= threshold are graduated
+       * range is 6-10 so steps of 100/5 = 20
+       */
+      int factor = col - THRESHOLD_FIVE;
+      Color expected = new Color(50 + 20 * factor, 200 - 20 * factor,
+              150 + 20 * factor);
+      Color result = testee.shadeCalculation(ann, col);
+      assertEquals(result, expected, "for column " + col);
+    }
+  }
+
+  /**
+   * Test the 'colour below threshold' case
+   */
+  @Test(groups = "Functional")
+  public void testShadeCalculation_belowThreshold()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
+
+    for (int col = 0; col < WIDTH; col++)
+    {
+      Color result = testee.shadeCalculation(ann, col);
+      /*
+       * colour is derived regardless of the threshold value 
+       * (the renderer will suppress colouring if above/below threshold)
+       */
+      Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+              150 + 10 * col);
+      assertEquals(result, expected, "for column " + col);
+    }
+
+    /*
+     * now make 0-5 the span of the colour range
+     * (annotation value == column number in this test)
+     */
+    testee.setThresholdIsMinMax(true);
+    for (int col = THRESHOLD_FIVE + 1; col < WIDTH; col++)
+    {
+      /*
+       * colours above the threshold are computed as before
+       */
+      Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+              150 + 10 * col);
+      Color result = testee.shadeCalculation(ann, col);
+      assertEquals(result, expected, "for column " + col);
+    }
+
+    for (int col = 0; col <= THRESHOLD_FIVE; col++)
+    {
+      /*
+       * colours for values <= threshold are graduated
+       * range is 0-5 so steps of 100/5 = 20
+       */
+      Color expected = new Color(50 + 20 * col, 200 - 20 * col,
+              150 + 20 * col);
+      Color result = testee.shadeCalculation(ann, col);
+      assertEquals(result, expected, "for column " + col);
+    }
+  }
+
+  /**
+   * Test the 'colour above threshold' case
+   */
+  @Test(groups = "Functional")
+  public void testFindColour_aboveThreshold()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.ABOVE_THRESHOLD);
+    testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+    for (int col = 0; col < WIDTH; col++)
+    {
+      Color result = testee.findColour('a', col, seq);
+      /*
+       * expect white below threshold of 5
+       */
+      Color expected = col < 5 ? Color.white : new Color(50 + 10 * col,
+              200 - 10 * col,
+              150 + 10 * col);
+      assertEquals(result, expected, "for column " + col);
+    }
+  
+    /*
+     * now make 6-10 the span of the colour range
+     * (annotation value == column number in this test)
+     */
+    testee.setThresholdIsMinMax(true);
+    for (int col = 0; col < WIDTH; col++)
+    {
+      /*
+       * colours for values >= threshold are graduated
+       * range is 6-10 so steps of 100/5 = 20
+       */
+      int factor = col - THRESHOLD_FIVE;
+      Color expected = col < 5 ? Color.white : new Color(50 + 20 * factor,
+              200 - 20 * factor,
+              150 + 20 * factor);
+      Color result = testee.findColour('a', col, seq);
+      assertEquals(result, expected, "for column " + col);
+    }
+  }
+
+  /**
+   * Test the 'colour below threshold' case
+   */
+  @Test(groups = "Functional")
+  public void testFindColour_belowThreshold()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
+    testee = (AnnotationColourGradient) testee.getInstance(al, null);
+  
+    for (int col = 0; col < WIDTH; col++)
+    {
+      Color result = testee.findColour('a', col, seq);
+      Color expected = col > 5 ? Color.white : new Color(50 + 10 * col,
+              200 - 10 * col, 150 + 10 * col);
+      assertEquals(result, expected, "for column " + col);
+    }
+  
+    /*
+     * now make 0-5 the span of the colour range
+     * (annotation value == column number in this test)
+     */
+    testee.setThresholdIsMinMax(true);
+    for (int col = 0; col < WIDTH; col++)
+    {
+      /*
+       * colours for values <= threshold are graduated
+       * range is 0-5 so steps of 100/5 = 20
+       */
+      Color expected = col > 5 ? Color.white : new Color(50 + 20 * col,
+              200 - 20 * col, 150 + 20 * col);
+      Color result = testee.findColour('a', col, seq);
+      assertEquals(result, expected, "for column " + col);
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testFindColour_noThreshold()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
+    testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+    for (int col = 0; col < WIDTH; col++)
+    {
+      Color result = testee.findColour('a', col, seq);
+      /*
+       * column <n> is n/10 of the way from minCol to maxCol
+       */
+      Color expected = new Color(50 + 10 * col, 200 - 10 * col,
+              150 + 10 * col);
+      assertEquals(result, expected, "for column " + col);
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testFindColour_originalColours()
+  {
+    AnnotationColourGradient testee = new AnnotationColourGradient(ann,
+            minColour, maxColour, AnnotationColourGradient.NO_THRESHOLD);
+    testee = (AnnotationColourGradient) testee.getInstance(al, null);
+
+    /*
+     * flag corresponding to 'use original colours' checkbox
+     * - just use the individual annotation colours
+     */
+    testee.setPredefinedColours(true);
+
+    /*
+     * the annotation colour is returned, except for column 0 where it is
+     * black - in this case the colour scheme colour overrides it
+     */
+    for (int col = 0; col < WIDTH; col++)
+    {
+      int hue = col * 20;
+      Color c = col == 0 ? minColour : new Color(hue, hue, hue);
+      assertEquals(testee.findColour('a', col, seq), c, "for column " + col);
+    }
+  }
+}
diff --git a/test/jalview/schemes/ColourSchemesTest.java b/test/jalview/schemes/ColourSchemesTest.java
index 4618ed7..0aaa38c 100644
--- a/test/jalview/schemes/ColourSchemesTest.java
+++ b/test/jalview/schemes/ColourSchemesTest.java
@@ -228,9 +228,9 @@ public class ColourSchemesTest
      * set and check Taylor colours
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Taylor.toString());
-    Color taylor1 = sr.getResidueBoxColour(seq, 88); // E 255,0,102
-    Color taylor2 = sr.getResidueBoxColour(seq, 89); // A 204,255,0
-    Color taylor3 = sr.getResidueBoxColour(seq, 90); // G 255,153,0
+    Color taylor1 = sr.getResidueColour(seq, 88, null); // E 255,0,102
+    Color taylor2 = sr.getResidueColour(seq, 89, null); // A 204,255,0
+    Color taylor3 = sr.getResidueColour(seq, 90, null); // G 255,153,0
     assertEquals(taylor1, new Color(255, 0, 102));
     assertEquals(taylor2, new Color(204, 255, 0));
     assertEquals(taylor3, new Color(255, 153, 0));
@@ -239,9 +239,9 @@ public class ColourSchemesTest
      * set and check Zappo colours
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Zappo.toString());
-    Color zappo1 = sr.getResidueBoxColour(seq, 88); // E red
-    Color zappo2 = sr.getResidueBoxColour(seq, 89); // A pink
-    Color zappo3 = sr.getResidueBoxColour(seq, 90); // G magenta
+    Color zappo1 = sr.getResidueColour(seq, 88, null); // E red
+    Color zappo2 = sr.getResidueColour(seq, 89, null); // A pink
+    Color zappo3 = sr.getResidueColour(seq, 90, null); // G magenta
     assertEquals(zappo1, Color.red);
     assertEquals(zappo2, Color.pink);
     assertEquals(zappo3, Color.magenta);
@@ -250,9 +250,9 @@ public class ColourSchemesTest
      * set 'stripy' colours - odd columns are Taylor and even are Zappo 
      */
     af.changeColour_actionPerformed("stripy");
-    Color stripy1 = sr.getResidueBoxColour(seq, 88);
-    Color stripy2 = sr.getResidueBoxColour(seq, 89);
-    Color stripy3 = sr.getResidueBoxColour(seq, 90);
+    Color stripy1 = sr.getResidueColour(seq, 88, null);
+    Color stripy2 = sr.getResidueColour(seq, 89, null);
+    Color stripy3 = sr.getResidueColour(seq, 90, null);
     assertEquals(stripy1, zappo1);
     assertEquals(stripy2, taylor2);
     assertEquals(stripy3, zappo3);
@@ -261,9 +261,9 @@ public class ColourSchemesTest
      * set and check Clustal colours
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString());
-    Color clustal1 = sr.getResidueBoxColour(seq, 88);
-    Color clustal2 = sr.getResidueBoxColour(seq, 89);
-    Color clustal3 = sr.getResidueBoxColour(seq, 90);
+    Color clustal1 = sr.getResidueColour(seq, 88, null);
+    Color clustal2 = sr.getResidueColour(seq, 89, null);
+    Color clustal3 = sr.getResidueColour(seq, 90, null);
     assertEquals(clustal1, ClustalColour.MAGENTA.colour);
     assertEquals(clustal2, ClustalColour.BLUE.colour);
     assertEquals(clustal3, ClustalColour.ORANGE.colour);
@@ -272,9 +272,9 @@ public class ColourSchemesTest
      * set 'MyClustal' colours - uses AWT colour equivalents
      */
     af.changeColour_actionPerformed("MyClustal");
-    Color myclustal1 = sr.getResidueBoxColour(seq, 88);
-    Color myclustal2 = sr.getResidueBoxColour(seq, 89);
-    Color myclustal3 = sr.getResidueBoxColour(seq, 90);
+    Color myclustal1 = sr.getResidueColour(seq, 88, null);
+    Color myclustal2 = sr.getResidueColour(seq, 89, null);
+    Color myclustal3 = sr.getResidueColour(seq, 90, null);
     assertEquals(myclustal1, Color.MAGENTA);
     assertEquals(myclustal2, Color.BLUE);
     assertEquals(myclustal3, Color.ORANGE);
diff --git a/test/jalview/structure/AtomSpecTest.java b/test/jalview/structure/AtomSpecTest.java
new file mode 100644
index 0000000..ea53131
--- /dev/null
+++ b/test/jalview/structure/AtomSpecTest.java
@@ -0,0 +1,74 @@
+package jalview.structure;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.fail;
+
+import org.testng.annotations.Test;
+
+public class AtomSpecTest
+{
+  @Test
+  public void testFromChimeraAtomSpec()
+  {
+    AtomSpec as = AtomSpec.fromChimeraAtomspec("#1:12.B");
+    assertEquals(as.getModelNumber(), 1);
+    assertEquals(as.getPdbResNum(), 12);
+    assertEquals(as.getChain(), "B");
+    assertNull(as.getPdbFile());
+
+    // no model - default to zero
+    as = AtomSpec.fromChimeraAtomspec(":13.C");
+    assertEquals(as.getModelNumber(), 0);
+    assertEquals(as.getPdbResNum(), 13);
+    assertEquals(as.getChain(), "C");
+    assertNull(as.getPdbFile());
+
+    // model.submodel
+    as = AtomSpec.fromChimeraAtomspec("#3.2:15");
+    assertEquals(as.getModelNumber(), 3);
+    assertEquals(as.getPdbResNum(), 15);
+    assertEquals(as.getChain(), "");
+    assertNull(as.getPdbFile());
+
+    String spec = "3:12.B";
+    try
+    {
+      as = AtomSpec.fromChimeraAtomspec(spec);
+      fail("Expected exception for " + spec);
+    } catch (IllegalArgumentException e)
+    {
+      // ok
+    }
+
+    spec = "#3:12-14.B";
+    try
+    {
+      as = AtomSpec.fromChimeraAtomspec(spec);
+      fail("Expected exception for " + spec);
+    } catch (IllegalArgumentException e)
+    {
+      // ok
+    }
+
+    spec = "";
+    try
+    {
+      as = AtomSpec.fromChimeraAtomspec(spec);
+      fail("Expected exception for " + spec);
+    } catch (IllegalArgumentException e)
+    {
+      // ok
+    }
+
+    spec = null;
+    try
+    {
+      as = AtomSpec.fromChimeraAtomspec(spec);
+      fail("Expected exception for " + spec);
+    } catch (NullPointerException e)
+    {
+      // ok
+    }
+  }
+}
diff --git a/test/jalview/structure/StructureMappingTest.java b/test/jalview/structure/StructureMappingTest.java
new file mode 100644
index 0000000..f26c5f1
--- /dev/null
+++ b/test/jalview/structure/StructureMappingTest.java
@@ -0,0 +1,46 @@
+package jalview.structure;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import java.util.HashMap;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class StructureMappingTest
+{
+  @Test(groups = "Functional")
+  public void testgetPDBResNumRanges()
+  {
+    HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+
+    StructureMapping mapping = new StructureMapping(null, null, null, null,
+            map, null);
+
+    List<int[]> ranges = mapping.getPDBResNumRanges(1, 2);
+    assertTrue(ranges.isEmpty());
+
+    map.put(1, new int[] { 12, 20 }); // 1 maps to 12
+    ranges = mapping.getPDBResNumRanges(2, 3);
+    assertTrue(ranges.isEmpty());
+    ranges = mapping.getPDBResNumRanges(1, 2);
+    assertEquals(ranges.size(), 1);
+    assertEquals(ranges.get(0)[0], 12);
+    assertEquals(ranges.get(0)[1], 12);
+
+    map.put(2, new int[] { 13, 20 }); // 2 maps to 13
+    ranges = mapping.getPDBResNumRanges(1, 2);
+    assertEquals(ranges.size(), 1);
+    assertEquals(ranges.get(0)[0], 12);
+    assertEquals(ranges.get(0)[1], 13);
+
+    map.put(3, new int[] { 15, 20 }); // 3 maps to 15 - break
+    ranges = mapping.getPDBResNumRanges(1, 5);
+    assertEquals(ranges.size(), 2);
+    assertEquals(ranges.get(0)[0], 12);
+    assertEquals(ranges.get(0)[1], 13);
+    assertEquals(ranges.get(1)[0], 15);
+    assertEquals(ranges.get(1)[1], 15);
+  }
+}
diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 0422537..7ba22b4 100644
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -44,6 +44,7 @@ import jalview.structures.models.AAStructureBindingModel.SuperposeData;
 
 import java.awt.Color;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -169,9 +170,10 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      public void superposeStructures(AlignmentI[] als, int[] alm,
+      public String superposeStructures(AlignmentI[] als, int[] alm,
               ColumnSelection[] alc)
       {
+        return null;
       }
 
       @Override
@@ -181,14 +183,7 @@ public class AAStructureBindingModelTest
 
       @Override
       protected StructureMappingcommandSet[] getColourBySequenceCommands(
-              String[] files, SequenceRenderer sr, FeatureRenderer fr,
-              AlignmentI alignment)
-      {
-        return null;
-      }
-
-      @Override
-      public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+              String[] files, SequenceRenderer sr, AlignmentViewPanel avp)
       {
         return null;
       }
@@ -215,6 +210,13 @@ public class AAStructureBindingModelTest
       public void colourByCharge()
       {
       }
+
+      @Override
+      public FeatureRenderer getFeatureRenderer(
+              AlignmentViewPanel alignment)
+      {
+        return null;
+      }
     };
   }
 
@@ -234,11 +236,14 @@ public class AAStructureBindingModelTest
       structs[i] = testee.new SuperposeData(al.getWidth());
     }
     /*
-     * initialise array of 'superposable columns' to true (would be false for
+     * initialise BitSet of 'superposable columns' to true (would be false for
      * hidden columns)
      */
-    boolean[] matched = new boolean[al.getWidth()];
-    Arrays.fill(matched, true);
+    BitSet matched = new BitSet();
+    for (int i = 0; i < al.getWidth(); i++)
+    {
+      matched.set(i);
+    }
 
     int refStructure = testee
             .findSuperposableResidues(al, matched, structs);
@@ -248,12 +253,12 @@ public class AAStructureBindingModelTest
     /*
      * only ungapped, structure-mapped columns are superposable
      */
-    assertFalse(matched[0]); // gap in first sequence
-    assertTrue(matched[1]);
-    assertFalse(matched[2]); // gap in third sequence
-    assertFalse(matched[3]); // gap in fourth sequence
-    assertTrue(matched[4]);
-    assertTrue(matched[5]); // gap in second sequence
+    assertFalse(matched.get(0)); // gap in first sequence
+    assertTrue(matched.get(1));
+    assertFalse(matched.get(2)); // gap in third sequence
+    assertFalse(matched.get(3)); // gap in fourth sequence
+    assertTrue(matched.get(4));
+    assertTrue(matched.get(5)); // gap in second sequence
 
     assertEquals("1YCS", structs[0].pdbId);
     assertEquals("3A6S", structs[1].pdbId);
@@ -278,13 +283,17 @@ public class AAStructureBindingModelTest
       structs[i] = testee.new SuperposeData(al.getWidth());
     }
     /*
-     * initialise array of 'superposable columns' to true (would be false for
+     * initialise BitSet of 'superposable columns' to true (would be false for
      * hidden columns)
      */
-    boolean[] matched = new boolean[al.getWidth()];
-    Arrays.fill(matched, true);
+    BitSet matched = new BitSet();
+    for (int i = 0; i < al.getWidth(); i++)
+    {
+      matched.set(i);
+    }
+
     // treat column 5 of the alignment as hidden
-    matched[4] = false;
+    matched.clear(4);
 
     int refStructure = testee
             .findSuperposableResidues(al, matched, structs);
@@ -292,21 +301,11 @@ public class AAStructureBindingModelTest
     assertEquals(0, refStructure);
 
     // only ungapped, structure-mapped columns are not superposable
-    assertFalse(matched[0]);
-    assertTrue(matched[1]);
-    assertFalse(matched[2]);
-    assertFalse(matched[3]);
-    assertFalse(matched[4]); // superposable, but hidden, column
-    assertTrue(matched[5]);
-  }
-
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    return null;
-  }
-
-  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
-  {
-    return null;
+    assertFalse(matched.get(0));
+    assertTrue(matched.get(1));
+    assertFalse(matched.get(2));
+    assertFalse(matched.get(3));
+    assertFalse(matched.get(4)); // superposable, but hidden, column
+    assertTrue(matched.get(5));
   }
 }
diff --git a/test/jalview/viewmodel/OverviewDimensionsTest.java b/test/jalview/viewmodel/OverviewDimensionsTest.java
new file mode 100644
index 0000000..398fec3
--- /dev/null
+++ b/test/jalview/viewmodel/OverviewDimensionsTest.java
@@ -0,0 +1,1037 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.viewmodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+@Test(singleThreaded = true)
+public class OverviewDimensionsTest
+{
+  AlignmentI al;
+  OverviewDimensions od;
+
+  // cached widths and heights
+  int boxWidth;
+  int boxHeight;
+  int viewHeight;
+  int viewWidth;
+  int alheight;
+  int alwidth;
+
+  ViewportRanges vpranges;
+
+  Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+
+  ColumnSelection hiddenCols = new ColumnSelection();
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    al = gen.generate(157, 525, 123, 5, 5);
+  }
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    if (!hiddenRepSequences.isEmpty())
+    {
+      al.getHiddenSequences().showAll(hiddenRepSequences);
+    }
+    hiddenCols.revealAllHiddenColumns();
+    
+    vpranges = new ViewportRanges(al);
+    vpranges.setStartRes(0);
+    vpranges.setEndRes(62);
+    vpranges.setStartSeq(0);
+    vpranges.setEndSeq(17);
+
+    viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
+    viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
+
+    ColumnSelection hiddenCols = new ColumnSelection();
+
+    od = new OverviewDimensions(vpranges, true);
+    // Initial box sizing - default path through code
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+
+    mouseClick(od, 0, 0);
+    moveViewport(0, 0);
+
+    // calculate before hidden columns so we get absolute values
+    alheight = vpranges.getAbsoluteAlignmentHeight();
+    alwidth = vpranges.getAbsoluteAlignmentWidth();
+
+    boxWidth = Math.round((float) (vpranges.getEndRes()
+            - vpranges.getStartRes() + 1)
+            * od.getWidth() / alwidth);
+    boxHeight = Math.round((float) (vpranges.getEndSeq()
+            - vpranges.getStartSeq() + 1)
+            * od.getSequencesHeight() / alheight);
+  }
+
+  @AfterClass(alwaysRun = true)
+  public void cleanUp()
+  {
+    al = null;
+  }
+
+  /**
+   * Test that the OverviewDimensions constructor sets width and height
+   * correctly
+   */
+  @Test(groups = { "Functional" })
+  public void testConstructor()
+  {
+    SequenceI seqa = new Sequence("Seq1", "ABC");
+    SequenceI seqb = new Sequence("Seq2", "ABC");
+    SequenceI seqc = new Sequence("Seq3", "ABC");
+    SequenceI seqd = new Sequence("Seq4", "ABC");
+    SequenceI seqe = new Sequence("Seq5",
+            "ABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+    int defaultGraphHeight = 20;
+    int maxWidth = 400;
+    int minWidth = 120;
+    int maxSeqHeight = 300;
+    int minSeqHeight = 40;
+
+    // test for alignment with width > height
+    SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
+    Alignment al1 = new Alignment(seqs1);
+    ViewportRanges props = new ViewportRanges(al1);
+
+    OverviewDimensions od = new OverviewDimensions(props, true);
+    int scaledHeight = 267;
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), scaledHeight);
+    assertEquals(od.getWidth(), maxWidth);
+    assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
+
+    // test for alignment with width < height
+    SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
+    Alignment al2 = new Alignment(seqs2);
+    props = new ViewportRanges(al2);
+
+    od = new OverviewDimensions(props, true);
+    int scaledWidth = 300;
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), maxSeqHeight);
+    assertEquals(od.getWidth(), scaledWidth);
+    assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
+
+    // test for alignment with width > height and sequence height scaled below
+    // min value
+    SequenceI[] seqs3 = new SequenceI[] { seqe };
+    Alignment al3 = new Alignment(seqs3);
+    props = new ViewportRanges(al3);
+
+    od = new OverviewDimensions(props, true);
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), minSeqHeight);
+    assertEquals(od.getWidth(), maxWidth);
+    assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
+
+    // test for alignment with width < height and width scaled below min value
+    SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
+        seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
+    Alignment al4 = new Alignment(seqs4);
+    props = new ViewportRanges(al4);
+
+    od = new OverviewDimensions(props, true);
+    assertEquals(od.getGraphHeight(), defaultGraphHeight);
+    assertEquals(od.getSequencesHeight(), maxSeqHeight);
+    assertEquals(od.getWidth(), minWidth);
+    assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
+
+    Alignment al5 = new Alignment(seqs4);
+    props = new ViewportRanges(al5);
+
+    od = new OverviewDimensions(props, false);
+    assertEquals(od.getGraphHeight(), 0);
+    assertEquals(od.getSequencesHeight(), maxSeqHeight);
+    assertEquals(od.getWidth(), minWidth);
+    assertEquals(od.getHeight(), maxSeqHeight);
+  }
+
+  /**
+   * Test that validation after mouse adjustments to boxX and boxY sets box
+   * dimensions and scroll values correctly, when there are no hidden rows or
+   * columns.
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromMouseClick()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // negative boxX value reset to 0
+    mouseClick(od, -5, 10);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollRow(),
+            Math.round((float) 10 * alheight / od.getSequencesHeight()));
+    assertEquals(od.getScrollCol(), 0);
+
+    // negative boxY value reset to 0
+    mouseClick(od, 6, -2);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) 6 * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+
+    // overly large boxX value reset to width-boxWidth
+    mouseClick(od, 100, 6);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+    assertEquals(od.getBoxY(), 6);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
+
+    // overly large boxY value reset to sequenceHeight - boxHeight
+    mouseClick(od, 10, 520);
+    assertEquals(od.getBoxX(), 10);
+    assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+
+    // here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
+    // and round rounds to 508; however we get 507 working with row values
+    // hence the subtraction of 1
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()) - 1);
+
+    // click past end of alignment, as above
+    mouseClick(od, 3000, 5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
+
+    // move viewport so startRes non-zero and then mouseclick
+    moveViewportH(50);
+
+    // click at viewport position
+    int oldboxx = od.getBoxX();
+    int oldboxy = od.getBoxY();
+    mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
+    assertEquals(od.getBoxX(), oldboxx + 5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getBoxY(), oldboxy + 2);
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
+
+    // click at top corner
+    mouseClick(od, 0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden cols at the start
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenColsAtStart()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide cols at start and check updated box position is correct
+    // changes boxX but not boxwidth
+    int lastHiddenCol = 30;
+    hiddenCols.hideColumns(0, lastHiddenCol);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+                    / alwidth));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // try to click in hidden cols, check box does not move
+    int xpos = 10;
+    mouseClick(od, xpos, 0);
+    assertEquals(
+            od.getBoxX(),
+            Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+                    / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(), 0);
+
+    // click to right of hidden columns, box moves to click point
+    testBoxIsAtClickPoint(40, 0);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) 40 * alwidth / od.getWidth())
+                    - (lastHiddenCol + 1));
+
+    // click to right of hidden columns such that box runs over right hand side
+    // of alignment
+    // box position is adjusted away from the edge
+    // overly large boxX value reset to width-boxWidth
+    xpos = 100;
+    mouseClick(od, xpos, 5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+    assertEquals(od.getBoxY(), 5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth())
+                    - (lastHiddenCol + 1));
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden cols in the middle
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenColsInMiddle()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+    
+    // hide columns 63-73, no change to box position or dimensions
+    int firstHidden = 63;
+    int lastHidden = 73;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // move box so that it overlaps with hidden cols on one side
+    // box width changes, boxX and scrollCol as for unhidden case
+    int xpos = 55 - boxWidth; // 55 is position in overview approx halfway
+                              // between cols 60 and 70
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round(xpos * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+
+    // move box so that it completely covers hidden cols
+    // box width changes, boxX and scrollCol as for hidden case
+    xpos = 33;
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+                    * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) xpos * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+
+    // move box so boxX is in hidden cols, box overhangs at right
+    // boxX and scrollCol at left of hidden area, box width extends across
+    // hidden region
+    xpos = 50;
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            boxWidth
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), firstHidden - 1);
+    assertEquals(od.getScrollRow(), 0);
+
+    // move box so boxX is to right of hidden cols, but does not go beyond full
+    // width of alignment
+    // box width, boxX and scrollCol all as for non-hidden case
+    xpos = 75;
+    testBoxIsAtClickPoint(xpos, 0);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(),
+            Math.round(xpos * alwidth / od.getWidth())
+                    - (lastHidden - firstHidden + 1));
+    
+    // move box so it goes beyond full width of alignment
+    // boxX, scrollCol adjusted back, box width normal
+    xpos = 3000;
+    mouseClick(od, xpos, 5);
+    assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+    assertEquals(od.getBoxY(), 5);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
+                    - (lastHidden - firstHidden + 1)));
+    assertEquals(od.getScrollRow(),
+            Math.round((float) od.getBoxY() * alheight
+                    / od.getSequencesHeight()));
+
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden cols at the end of
+   * the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenColsAtEnd()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide columns 140-164, no change to box position or dimensions
+    int firstHidden = 140;
+    int lastHidden = 164;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // click to left of hidden cols, without overlapping
+    // boxX, scrollCol and width as normal
+    int xpos = 5;
+    testBoxIsAtClickPoint(xpos, 0);
+    assertEquals(od.getScrollRow(), 0);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) xpos * alwidth / od.getWidth()));
+
+    // click to left of hidden cols, with overlap
+    // boxX and scrollCol adjusted for hidden cols, width normal
+    xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
+    mouseClick(od, xpos, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+                    - boxWidth + 1);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+
+    // click in hidden cols
+    // boxX and scrollCol adjusted for hidden cols, width normal
+    xpos = 115;
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+                    - boxWidth + 1);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+
+    // click off end of alignment
+    // boxX and scrollCol adjusted for hidden cols, width normal
+    xpos = 3000;
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+                    - boxWidth + 1);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(),
+            Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+    assertEquals(od.getScrollRow(), 0);
+  }
+
+  /**
+   * Test that the box position is set correctly when set from the viewport,
+   * with no hidden rows or columns
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewport()
+  {
+    // move viewport to start of alignment
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to right
+    moveViewportH(70);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 70 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport down
+    moveViewportV(100);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 70 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(),
+            Math.round(100 * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to bottom right
+    moveViewport(98, 508);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 98 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(),
+            Math.round((float) 508 * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden columns
+   * at the start
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenColsAtStart()
+  {
+    int firstHidden = 0;
+    int lastHidden = 20;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    // move viewport to start of alignment
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to end of alignment - need to make startRes by removing
+    // hidden cols because of how viewport/overview are implemented
+    moveViewport(98 - lastHidden - 1, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 98 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden columns
+   * in the middle
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenColsInMiddle()
+  {
+    int firstHidden = 68;
+    int lastHidden = 78;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    // move viewport before hidden columns
+    moveViewport(3, 0);
+
+    assertEquals(od.getBoxX(),
+            Math.round((float) 3 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    System.out.println(od.getBoxWidth());
+    assertEquals(od.getBoxWidth(), boxWidth);
+    System.out.println(od.getBoxWidth());
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to left of hidden columns with overlap
+    moveViewport(10, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 10 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            boxWidth
+                    + Math.round((float) (lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to straddle hidden columns
+    moveViewport(63, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 63 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(
+            od.getBoxWidth(),
+            boxWidth
+                    + Math.round((lastHidden - firstHidden + 1)
+                            * od.getWidth() / alwidth));
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to right of hidden columns, no overlap
+    moveViewport(80 - (lastHidden - firstHidden + 1), 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 80 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden columns
+   * at the end
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenColsAtEnd()
+  {
+    int firstHidden = 152;
+    int lastHidden = 164;
+    hiddenCols.hideColumns(firstHidden, lastHidden);
+
+    // move viewport before hidden columns
+    moveViewport(3, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) 3 * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to hidden columns
+    // viewport can't actually extend into hidden cols,
+    // so move to the far right edge of the viewport
+    moveViewport(firstHidden - viewWidth, 0);
+    assertEquals(od.getBoxX(),
+            Math.round((float) (firstHidden - viewWidth)
+                    * od.getWidth() / alwidth));
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden rows at
+   * the start
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenRowsAtStart()
+  {
+    int firstHidden = 0;
+    int lastHidden = 20;
+    hideSequences(firstHidden, lastHidden);
+
+    // move viewport to start of alignment:
+    // box moves to below hidden rows, height remains same
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
+                    / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to end of alignment
+    moveViewport(0, 525 - viewHeight - lastHidden - 1);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (525 - viewHeight) * od.getSequencesHeight()
+                    / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden rows in
+   * the middle
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenRowsInMiddle()
+  {
+    int firstHidden = 200;
+    int lastHidden = 210;
+    hideSequences(firstHidden, lastHidden);
+
+    // move viewport to start of alignment:
+    // box, height etc as in non-hidden case
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to straddle hidden rows
+    moveViewport(0, 198);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
+            / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(
+            od.getBoxHeight(),
+            Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
+                    * od.getSequencesHeight() / alheight));
+  }
+
+  /**
+   * Test that the box position is set correctly when there are hidden rows at
+   * the bottom
+   */
+  @Test(groups = { "Functional" })
+  public void testSetBoxFromViewportHiddenRowsAtEnd()
+  {
+    int firstHidden = 500;
+    int lastHidden = 524;
+    hideSequences(firstHidden, lastHidden);
+
+    // move viewport to start of alignment:
+    // box, height etc as in non-hidden case
+    moveViewport(0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // move viewport to end of alignment
+    // viewport sits above hidden rows and does not include them
+    moveViewport(0, firstHidden - viewHeight - 1);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (firstHidden - viewHeight - 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the start
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsAtStart()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide rows at start and check updated box position is correct
+    // changes boxY but not boxheight
+    int lastHiddenRow = 30;
+    hideSequences(0, lastHiddenRow);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) (lastHiddenRow + 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click in hidden rows - same result
+    mouseClick(od, 0, 0);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (lastHiddenRow + 1)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click below hidden rows
+    mouseClick(od, 0, 150);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 150);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the middle
+   * of the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsInMiddle()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide rows in middle and check updated box position is correct
+    // no changes
+    int firstHiddenRow = 50;
+    int lastHiddenRow = 54;
+    hideSequences(firstHiddenRow, lastHiddenRow);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click above hidden rows, so that box overlaps
+    int ypos = 35; // column value in residues
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(
+            od.getBoxHeight(),
+            boxHeight
+                    + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+                            * od.getSequencesHeight() / alheight));
+
+    // click so that box straddles hidden rows
+    ypos = 44; // column value in residues
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(
+            od.getBoxHeight(),
+            boxHeight
+                    + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+                            * od.getSequencesHeight() / alheight));
+  }
+
+  /**
+   * Test setting of the box position, when there are hidden rows at the end of
+   * the alignment
+   */
+  @Test(groups = { "Functional" })
+  public void testFromMouseWithHiddenRowsAtEnd()
+  {
+    od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+    assertEquals(od.getScrollCol(), 0);
+    assertEquals(od.getScrollRow(), 0);
+
+    // hide rows at end and check updated box position is correct
+    // no changes
+    int firstHidden = 500;
+    int lastHidden = 524;
+    hideSequences(firstHidden, lastHidden);
+
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(), 0);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click above hidden rows
+    int ypos = 40; // row 40
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(od.getBoxY(),
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click above hidden rows so box overlaps
+    // boxY moved upwards, boxHeight remains same
+    ypos = 497; // row 497
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((float) (firstHidden - viewHeight)
+                    * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+    // click within hidden rows
+    ypos = 505;
+    mouseClick(od, 0,
+            Math.round((float) ypos * od.getSequencesHeight() / alheight));
+    assertEquals(od.getBoxX(), 0);
+    assertEquals(
+            od.getBoxY(),
+            Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
+                    / alheight));
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+  }
+
+  /*
+   * Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
+   */
+  private void moveViewportH(int startRes)
+  {
+    vpranges.setStartRes(startRes);
+    vpranges.setEndRes(startRes + viewWidth - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+  }
+
+  /*
+   * Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
+   */
+  private void moveViewportV(int startSeq)
+  {
+    vpranges.setStartSeq(startSeq);
+    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+  }
+
+  /*
+   * Move viewport horizontally and vertically.
+   */
+  private void moveViewport(int startRes, int startSeq)
+  {
+    vpranges.setStartRes(startRes);
+    vpranges.setEndRes(startRes + viewWidth - 1);
+    vpranges.setStartSeq(startSeq);
+    vpranges.setEndSeq(startSeq + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+  }
+
+  /*
+   * Mouse click as position x,y in overview window
+   */
+  private void mouseClick(OverviewDimensions od, int x, int y)
+  {
+    od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols,
+            vpranges);
+
+    // updates require an OverviewPanel to exist which it doesn't here
+    // so call setBoxPosition() as it would be called by the AlignmentPanel
+    // normally
+
+    vpranges.setStartRes(od.getScrollCol());
+    vpranges.setEndRes(od.getScrollCol() + viewWidth - 1);
+    vpranges.setStartSeq(od.getScrollRow());
+    vpranges.setEndSeq(od.getScrollRow() + viewHeight - 1);
+    od.setBoxPosition(al.getHiddenSequences(), hiddenCols, vpranges);
+  }
+  
+  /*
+   * Test that the box is positioned with the top left corner at xpos, ypos
+   * and with the original width and height
+   */
+  private void testBoxIsAtClickPoint(int xpos, int ypos)
+  {
+    mouseClick(od, xpos, ypos);
+    assertEquals(od.getBoxX(), xpos);
+    assertEquals(od.getBoxY(), ypos);
+    assertEquals(od.getBoxWidth(), boxWidth);
+    assertEquals(od.getBoxHeight(), boxHeight);
+
+  }
+
+  /*
+   * Hide sequences between start and end
+   */
+  private void hideSequences(int start, int end)
+  {
+    SequenceI[] allseqs = al.getSequencesArray();
+    SequenceGroup theseSeqs = new SequenceGroup();
+    
+    for (int i = start; i <= end; i++)
+    {
+      theseSeqs.addSequence(allseqs[i], false);
+      al.getHiddenSequences().hideSequence(allseqs[i]);
+    }
+
+    hiddenRepSequences.put(allseqs[start], theseSeqs);
+  }
+}
diff --git a/test/jalview/viewmodel/ViewportRangesTest.java b/test/jalview/viewmodel/ViewportRangesTest.java
new file mode 100644
index 0000000..cfd03cd
--- /dev/null
+++ b/test/jalview/viewmodel/ViewportRangesTest.java
@@ -0,0 +1,100 @@
+package jalview.viewmodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.analysis.AlignmentGenerator;
+import jalview.datamodel.AlignmentI;
+
+import org.testng.annotations.Test;
+
+public class ViewportRangesTest {
+
+  AlignmentGenerator gen = new AlignmentGenerator(false);
+
+  AlignmentI al = gen.generate(20, 30, 1, 5, 5);
+
+  @Test
+  public void testViewportRanges() 
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    
+    assertEquals(vr.getStartRes(),0);
+    assertEquals(vr.getEndRes(), al.getWidth()-1);
+    assertEquals(vr.getStartSeq(), 0);
+    assertEquals(vr.getEndSeq(), al.getHeight() - 1);
+  }
+
+  @Test
+  public void testGetAbsoluteAlignmentHeight()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+
+    assertEquals(vr.getAbsoluteAlignmentHeight(), al.getHeight());
+
+    al.getHiddenSequences().hideSequence(al.getSequenceAt(3));
+    assertEquals(vr.getAbsoluteAlignmentHeight(), al.getHeight() + 1);
+  }
+
+  @Test
+  public void testGetAbsoluteAlignmentWidth()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    assertEquals(vr.getAbsoluteAlignmentWidth(), al.getWidth());
+  }
+
+  @Test
+  public void testSetEndRes()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setEndRes(-1);
+    assertEquals(vr.getEndRes(), 0);
+
+    vr.setEndRes(al.getWidth());
+    assertEquals(vr.getEndRes(), al.getWidth() - 1);
+
+    vr.setEndRes(al.getWidth() - 1);
+    assertEquals(vr.getEndRes(), al.getWidth() - 1);
+  }
+
+  @Test
+  public void testSetEndSeq()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setEndSeq(-1);
+    assertEquals(vr.getEndSeq(), 0);
+
+    vr.setEndSeq(al.getHeight());
+    assertEquals(vr.getEndSeq(), al.getHeight() - 1);
+
+    vr.setEndRes(al.getHeight() - 1);
+    assertEquals(vr.getEndSeq(), al.getHeight() - 1);
+  }
+
+  @Test
+  public void testSetStartRes()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setStartRes(-1);
+    assertEquals(vr.getStartRes(), 0);
+
+    vr.setStartRes(al.getWidth());
+    assertEquals(vr.getStartRes(), al.getWidth() - 1);
+
+    vr.setStartRes(al.getWidth() - 1);
+    assertEquals(vr.getStartRes(), al.getWidth() - 1);
+  }
+
+  @Test
+  public void testSetStartSeq()
+  {
+    ViewportRanges vr = new ViewportRanges(al);
+    vr.setStartSeq(-1);
+    assertEquals(vr.getStartSeq(), 0);
+
+    vr.setStartSeq(al.getHeight());
+    assertEquals(vr.getStartSeq(), al.getHeight() - 1);
+
+    vr.setStartSeq(al.getHeight() - 1);
+    assertEquals(vr.getStartSeq(), al.getHeight() - 1);
+  }
+}
diff --git a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java
index 98ca303..f1dafcb 100644
--- a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java
+++ b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java
@@ -20,9 +20,11 @@
  */
 package jalview.ws.seqfetcher;
 
+import static org.testng.Assert.assertTrue;
+
+import jalview.bin.Cache;
 import jalview.gui.JvOptionPane;
 
-import org.testng.AssertJUnit;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -36,15 +38,12 @@ public class DasSequenceFetcher
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Network" })
   public void testDasRegistryContact()
   {
-    jalview.bin.Cache.getDasSourceRegistry().refreshSources();
-    AssertJUnit
-            .assertTrue(
-                    "Expected to find at least one DAS source at the registry. Check config.",
-                    jalview.bin.Cache.getDasSourceRegistry().getSources()
-                            .size() > 0);
+    Cache.getDasSourceRegistry().refreshSources();
+    assertTrue(Cache.getDasSourceRegistry().getSources().isEmpty(),
+            "Expected to find no DAS sources at the registry. Check config.");
   }
 
 }
diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index d805e47..7f8adc9 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -38,6 +38,8 @@ import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
 
 import org.testng.Assert;
 import org.testng.FileAssert;
@@ -280,7 +282,19 @@ public class SiftsClientTest
               "A", testSeq, null);
       Assert.assertEquals(testSeq.getStart(), 1);
       Assert.assertEquals(testSeq.getEnd(), 147);
-      Assert.assertEquals(actualMapping, expectedMapping);
+      // Can't do Assert.assertEquals(actualMapping, expectedMapping);
+      // because this fails in our version of TestNG
+      Assert.assertEquals(actualMapping.size(), expectedMapping.size());
+      Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
+              .iterator();
+      while (it.hasNext())
+      {
+        Map.Entry<Integer, int[]> pair = it.next();
+        Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
+        Assert.assertEquals(actualMapping.get(pair.getKey()),
+                pair.getValue());
+      }
+
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -399,7 +413,21 @@ groups = { "Network" },
 
     Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
             expectedMappingOutput);
-    Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
+
+    // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
+    // because this fails in our version of TestNG
+    Assert.assertEquals(strucMapping.getMapping().size(),
+            expectedMapping.size());
+    Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
+            .iterator();
+    while (it.hasNext())
+    {
+      Map.Entry<Integer, int[]> pair = it.next();
+      Assert.assertTrue(strucMapping.getMapping()
+              .containsKey(pair.getKey()));
+      Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
+              pair.getValue());
+    }
   }
 
   @Test(groups = { "Network" })