From: jprocter <Jim Procter>
Date: Wed, 18 Aug 2010 10:15:01 +0000 (+0000)
Subject: refactor to abstract jmol/jalview binding and applet and application specific sequenc... 
X-Git-Tag: Release_2_6~124
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b32b824388dea3107cd1598d63f8759f00b75e1f;p=jalview.git

refactor to abstract jmol/jalview binding and applet and application specific sequence structure binding.
---

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 9809859..fb15c82 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -27,15 +27,15 @@ import jalview.structure.*;
 import jalview.io.*;
 
 import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
 
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 
 import jalview.schemes.*;
 
-public class AppletJmol extends EmbmenuFrame implements StructureListener,
-        JmolStatusListener, KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+public class AppletJmol extends EmbmenuFrame implements 
+// StructureListener,
+        KeyListener, ActionListener, ItemListener, SequenceStructureBinding
 
 {
   Menu fileMenu = new Menu("File");
@@ -74,22 +74,12 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
 
   MenuItem jmolHelp = new MenuItem("Jmol Help");
 
-  JmolViewer viewer;
-
-  JmolPopup jmolpopup;
-
   Panel scriptWindow;
 
   TextField inputLine;
 
   TextArea history;
 
-  SequenceI[] sequence;
-
-  String[] chains;
-
-  StructureSelectionManager ssm;
-
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
@@ -98,11 +88,11 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
 
   boolean loadedInline;
 
-  PDBEntry pdbentry;
+  // boolean colourBySequence = true;
 
-  boolean colourBySequence = true;
+  FeatureRenderer fr = null;
 
-  Vector atomsPicked = new Vector();
+  AppletJmolBinding jmb;
 
   /**
    * datasource protocol for access to PDBEntry
@@ -113,10 +103,9 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
           AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
-    this.sequence = seq;
-    this.chains = chains;
-    this.pdbentry = pdbentry;
-    this.protocol = protocol;
+    jmb = new AppletJmolBinding(this, new PDBEntry[]
+    { pdbentry }, seq, chains, protocol);
+    jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
       if (protocol.equals(AppletFormatAdapter.PASTE))
@@ -189,12 +178,10 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
     renderPanel = new RenderPanel();
     embedMenuIfNeeded(renderPanel);
     this.add(renderPanel, BorderLayout.CENTER);
-    viewer = JmolViewer.allocateViewer(renderPanel,
-            new SmarterJmolAdapter(), "jalviewJmol", ap.av.applet
-                    .getDocumentBase(), ap.av.applet.getCodeBase(), "",
-            this);
-
-    jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
+    jmb.allocateViewer(renderPanel, 
+            "jalviewJmol", ap.av.applet.getDocumentBase(), ap.av.applet
+                    .getCodeBase(), "");
+    jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -214,7 +201,7 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       else if (protocol.equals(AppletFormatAdapter.FILE)
               || protocol.equals(AppletFormatAdapter.URL))
       {
-        viewer.openFile(pdbentry.getFile());
+        jmb.viewer.openFile(pdbentry.getFile());
       }
       else
       {
@@ -257,7 +244,7 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
             throw new Exception(
                     "Invalid datasource. Could not obtain Reader.");
           }
-          viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
+          jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader);
         } catch (Exception e)
         {
           // give up!
@@ -269,28 +256,31 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       }
     }
 
-    jalview.bin.JalviewLite.addFrame(this, "Jmol", 400, 400);
+    jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
   }
 
   /**
-   * create a new binding between structures in an existing jmol viewer instance and
-   * an alignpanel with sequences that have existing PDBFile entries. Note, this does not open a new Jmol window, 
-   * or modify the display of the structures in the original jmol window.
+   * create a new binding between structures in an existing jmol viewer instance
+   * and an alignpanel with sequences that have existing PDBFile entries. Note,
+   * this does not open a new Jmol window, or modify the display of the
+   * structures in the original jmol window.
+   * 
    * @param viewer2
    * @param alignPanel
-   * @param seqs - sequences to search for associations
+   * @param seqs
+   *          - sequences to search for associations
    */
   public AppletJmol(JmolViewer viewer2, AlignmentPanel alignPanel,
           SequenceI[] seqs)
   {
-    
+
     // TODO Auto-generated constructor stub
   }
 
   public void loadInline(String string)
   {
     loadedInline = true;
-    viewer.openStringInline(string);
+    jmb.viewer.openStringInline(string);
   }
 
   void setChainMenuItems(Vector chains)
@@ -316,10 +306,9 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
 
   void centerViewer()
   {
-    jmolHistory(false);
-    StringBuffer cmd = new StringBuffer();
+    Vector toshow = new Vector();
     String lbl;
-    int mlength, p,mnum;
+    int mlength, p, mnum;
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -327,64 +316,22 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
         CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i);
         if (item.getState())
         {
-          lbl = item.getLabel();
-          mlength = 0;
-          do
-          {
-            p = mlength;
-            mlength = lbl.indexOf(":", p);
-          } while (p < mlength && mlength < (lbl.length() - 2));
-                  mnum = 1+getModelNum(lbl.substring(0, mlength));
-        if (mnum>0)
-          {cmd.append(":" + lbl.substring(mlength + 1) + " /"
-                + mnum + " or ");
-          }
+          toshow.addElement(item.getLabel());
         }
       }
     }
-
-    if (cmd.length() > 0)
-      cmd.setLength(cmd.length() - 4);
-
-    viewer
-            .evalString("select *;restrict " + cmd + ";cartoon;center "
-                    + cmd);
-    jmolHistory(true);
-  }
-
-  private int getModelNum(String modelFileName)
-  {
-    String[] mfn = getPdbFile();
-    if (mfn == null)
-    {
-      return -1;
-    }
-    for (int i = 0; i < mfn.length; i++)
-    {
-      if (mfn[i].equalsIgnoreCase(modelFileName))
-        return i;
-    }
-    return -1;
+    jmb.centerViewer(toshow);
   }
 
   void closeViewer()
   {
-    viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
-    // remove listeners for all structures in viewer
-    StructureSelectionManager.getStructureSelectionManager()
-            .removeStructureViewerListener(this, this.getPdbFile());
-    // and shut down jmol
-    viewer.evalStringQuiet("zap");
-    viewer.setJmolStatusListener(null);
-
-    viewer = null;
-
+    jmb.closeViewer();
+    jmb = null;
     this.setVisible(false);
   }
 
   public void actionPerformed(ActionEvent evt)
   {
-    jmolHistory(false);
     if (evt.getSource() == mappingMenuItem)
     {
       jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
@@ -394,54 +341,63 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
 
       jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
               550, 600);
-      cap.setText(StructureSelectionManager.getStructureSelectionManager()
-              .printMapping(pdbentry.getFile()));
+      StringBuffer sb = new StringBuffer();
+      for (int s = 0; s < jmb.pdbentry.length; s++)
+      {
+        sb.append(StructureSelectionManager.getStructureSelectionManager()
+                .printMapping(jmb.pdbentry[s].getFile()));
+        sb.append("\n");
+      }
     }
     else if (evt.getSource() == charge)
     {
-      colourBySequence = false;
-      seqColour.setState(false);
-      viewer
-              .evalStringQuiet("select *;color white;select ASP,GLU;color red;"
-                      + "select LYS,ARG;color blue;select CYS;color yellow");
+      setEnabled(charge);
+      jmb.colourByCharge();
     }
 
     else if (evt.getSource() == chain)
     {
-      colourBySequence = false;
-      seqColour.setState(false);
-      viewer.evalStringQuiet("select *;color chain");
+      setEnabled(chain);
+      jmb.colourByChain();
     }
     else if (evt.getSource() == zappo)
     {
-      setJalviewColourScheme(new ZappoColourScheme());
+      setEnabled(zappo);
+      jmb.setJalviewColourScheme(new ZappoColourScheme());
     }
     else if (evt.getSource() == taylor)
     {
-      setJalviewColourScheme(new TaylorColourScheme());
+      setEnabled(taylor);
+      jmb.setJalviewColourScheme(new TaylorColourScheme());
     }
     else if (evt.getSource() == hydro)
     {
-      setJalviewColourScheme(new HydrophobicColourScheme());
+      setEnabled(hydro);
+      jmb.setJalviewColourScheme(new HydrophobicColourScheme());
     }
     else if (evt.getSource() == helix)
     {
-      setJalviewColourScheme(new HelixColourScheme());
+      setEnabled(helix);
+      jmb.setJalviewColourScheme(new HelixColourScheme());
     }
     else if (evt.getSource() == strand)
     {
-      setJalviewColourScheme(new StrandColourScheme());
+      setEnabled(strand);
+      jmb.setJalviewColourScheme(new StrandColourScheme());
     }
     else if (evt.getSource() == turn)
     {
-      setJalviewColourScheme(new TurnColourScheme());
+      setEnabled(turn);
+      jmb.setJalviewColourScheme(new TurnColourScheme());
     }
     else if (evt.getSource() == buried)
     {
-      setJalviewColourScheme(new BuriedColourScheme());
+      setEnabled(buried);
+      jmb.setJalviewColourScheme(new BuriedColourScheme());
     }
     else if (evt.getSource() == user)
     {
+      setEnabled(user);
       new UserDefinedColours(this);
     }
     else if (evt.getSource() == jmolHelp)
@@ -464,54 +420,30 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
         if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
           ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
       }
+
       centerViewer();
       allChainsSelected = false;
     }
-    jmolHistory(true);
   }
-  private void jmolHistory(boolean enable)
-  {
-    viewer.setBooleanProperty("history", enable);
-  }
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    colourBySequence = false;
-    seqColour.setState(false);
-
-    if (cs == null)
-      return;
-
-    String res;
-    int index;
-    Color col;
-    jmolHistory(false);
-
-    Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
-    while (en.hasMoreElements())
-    {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if (index > 20)
-        continue;
-
-      col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
-      command.append("select " + res + ";color[" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
-    }
 
-    viewer.evalStringQuiet(command.toString());
-    jmolHistory(true);
+  /**
+   * tick or untick the seqColour menu entry depending upon if it was selected or not.
+   * @param itm
+   */
+  private void setEnabled(MenuItem itm)
+  {
+    seqColour.setState(itm==seqColour);
+    jmb.setColourBySequence(itm==seqColour);
   }
 
   public void itemStateChanged(ItemEvent evt)
   {
     if (evt.getSource() == seqColour)
     {
-      lastCommand = null;
-      colourBySequence = seqColour.getState();
-      colourBySequence(ap);
+      setEnabled(seqColour);
+      jmb
+              .colourBySequence(ap.av.getShowSequenceFeatures(),
+                      ap.av.alignment);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -521,7 +453,7 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
   {
     if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
     {
-      viewer.evalString(inputLine.getText());
+      jmb.eval(inputLine.getText());
       history.append("\n$ " + inputLine.getText());
       inputLine.setText("");
     }
@@ -536,461 +468,23 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
   {
   }
 
-  String[] modelFileNames = null;
-
-  // ////////////////////////////////
-  // /StructureListener
-  public String[] getPdbFile()
-  {
-    if (modelFileNames == null)
-    {
-      String mset[] = new String[viewer.getModelCount()];
-      for (int i = 0; i < mset.length; i++)
-      {
-        mset[i] = viewer.getModelFileName(i);
-      }
-      modelFileNames = mset;
-    }
-    return modelFileNames;
-  }
-
-  String lastMessage;
-
-  // jmol/ssm only
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    int pdbResNum;
-    int mdlSep = strInfo.indexOf("/");
-    int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
-    if (chainSeparator == -1)
-    {
-      chainSeparator = strInfo.indexOf(".");
-      if (mdlSep > -1 && mdlSep < chainSeparator)
-      {
-        chainSeparator1 = chainSeparator;
-        chainSeparator = mdlSep;
-      }
-    }
-    pdbResNum = Integer.parseInt(strInfo.substring(
-            strInfo.indexOf("]") + 1, chainSeparator));
-
-    String chainId;
-
-    if (strInfo.indexOf(":") > -1)
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
-              .indexOf("."));
-    else
-    {
-      chainId = " ";
-    }
-
-    String pdbfilename = pdbentry.getFile();
-    if (mdlSep > -1)
-    {
-      if (chainSeparator1 == -1)
-      {
-        chainSeparator1 = strInfo.indexOf(".", mdlSep);
-      }
-      String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
-              chainSeparator1) : strInfo.substring(mdlSep + 1);
-      try
-      {
-        // recover PDB filename for the model hovered over.
-        pdbfilename = viewer
-                .getModelFileName(new Integer(mdlId).intValue() - 1);
-      } catch (Exception e)
-      {
-      }
-      ;
-    }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
-    lastMessage = strInfo;
-  }
-
-  StringBuffer resetLastRes = new StringBuffer();
-
-  StringBuffer eval = new StringBuffer();
-
-  // jmol/ssm only
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    int mdlNum = 1+getModelNum(pdbfile);
-    if (mdlNum==0)
-    {
-      return;
-    }
-
-    jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
-
-    eval.setLength(0);
-    eval.append("select " + pdbResNum); // +modelNum
-
-    resetLastRes.setLength(0);
-    resetLastRes.append("select " + pdbResNum); // +modelNum
-
-    if (!chain.equals(" "))
-    {
-    eval.append(":");
-    resetLastRes.append(":");
-      eval.append(chain);
-      resetLastRes.append(chain);
-    }
-    // if (mdlNum != 0)
-    {
-      eval.append(" /" + (mdlNum));
-      resetLastRes.append("/" + (mdlNum));
-    }
-    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
-    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + " and not hetero; spacefill 0;");
-
-    eval.append("spacefill 200;select none");
-
-    viewer.evalStringQuiet(eval.toString());
-    jmolHistory(true);
-
-  }
-
   public void updateColours(Object source)
   {
-    colourBySequence((AlignmentPanel) source);
-  }
-
-  // End StructureListener
-  // //////////////////////////
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (!pdbfile.equals(pdbentry.getFile()))
-      return null;
-
-    return new Color(viewer.getAtomArgb(atomIndex));
-  }
-
-  String lastCommand;
-
-  FeatureRenderer fr = null;
-
-  public void colourBySequence(AlignmentPanel sourceap)
-  {
-    this.ap = sourceap;
-
-    if (!colourBySequence)
-      return;
-    String[] files = getPdbFile();
-    SequenceRenderer sr = new SequenceRenderer(ap.av);
-
-    boolean showFeatures = false;
-
-    if (ap.av.showSequenceFeatures)
-    {
-      showFeatures = true;
-      if (fr == null)
-      {
-        fr = new jalview.appletgui.FeatureRenderer(ap.av);
-      }
-
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    StringBuffer command = new StringBuffer();
-
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-    {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
-      if (mapping == null || mapping.length < 1)
-        continue;
-
-      int lastPos = -1;
-      for (int s = 0; s < sequence.length; s++)
-      {
-        for (int sp, m = 0; m < mapping.length; m++)
-        {
-          if (mapping[m].getSequence() == sequence[s]
-                  && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
-          {
-            SequenceI asp = ap.av.alignment.getSequenceAt(sp);
-            for (int r = 0; r < asp.getLength(); r++)
-            {
-              // no mapping to gaps in sequence
-              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
-              {
-                continue;
-              }
-              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
-              if (pos < 1 || pos == lastPos)
-                continue;
-
-              lastPos = pos;
-
-              Color col = sr.getResidueBoxColour(sequence[s], r);
-
-              if (showFeatures)
-                col = fr.findFeatureColour(col, sequence[s], r);
-              String newSelcom = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
-                      + col.getBlue() + "]";
-              if (command.toString().endsWith(newSelcom))
-              {
-                command = condenseCommand(command.toString(), pos);
-                continue;
-              }
-              // TODO: deal with case when buffer is too large for Jmol to parse
-              // - execute command and flush
-
-              command.append(";select " + pos);
-              command.append(newSelcom);
-            }
-            break;
-          }
-        }
-      }
-    }
-
-    jmolHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command.toString()))
-    {
-      viewer.evalStringQuiet(command.toString());
-    }
-    jmolHistory(true);
-    lastCommand = command.toString();
-  }
-
-  StringBuffer condenseCommand(String command, int pos)
-  {
-
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
-
-    command = command.substring(sb.length());
-
-    String start;
-
-    if (command.indexOf("-") > -1)
-    {
-      start = command.substring(0, command.indexOf("-"));
-    }
-    else
-    {
-      start = command.substring(0, command.indexOf(":"));
-    }
-
-    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
-    return sb;
-  }
-
-  // ///////////////////////////////
-  // JmolStatusListener
-
-  public String eval(String strEval)
-  {
-    // System.out.println(strEval);
-    // "# 'eval' is implemented only for the applet.";
-    return null;
-  }
-
-  public void createImage(String file, String type, int quality)
-  {
+    AlignmentPanel ap = (AlignmentPanel) source;
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
   }
 
-  public void notifyFileLoaded(String fullPathName, String fileName2,
-          String modelName, String errorMsg, int modelParts)
+  public void updateTitleAndMenus()
   {
-    if (errorMsg != null)
+    if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
     {
-      fileLoadingError = errorMsg;
       repaint();
       return;
     }
-    fileLoadingError = null;
-    modelFileNames = null;
-    
-    String[] modelfilenames = getPdbFile();
-    ssm = StructureSelectionManager.getStructureSelectionManager();
-    boolean modelsloaded=false;
-    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
-    {
-      String fileName = modelfilenames[modelnum];
-      if (fileName != null)
-      {
-        // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
-        if (pdbentry.getFile().equals(fileName))
-        {
-          modelsloaded=true;
-          MCview.PDBfile pdb;
-          if (loadedInline)
-          {
-            pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
-                    AppletFormatAdapter.PASTE);
-            pdbentry.setFile("INLINE" + pdb.id);
-          }
-          else
-          {
-            // TODO: Jmol can in principle retrieve from CLASSLOADER but this
-            // needs
-            // to be tested. See mantis bug
-            // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-
-            pdb = ssm.setMapping(sequence, chains, pdbentry.getFile(),
-                    AppletFormatAdapter.URL);
-
-          }
-
-          pdbentry.setId(pdb.id);
-
-          Vector chains = new Vector();
-          for (int i = 0; i < pdb.chains.size(); i++)
-          {
-            chains.addElement(new String(pdb.id + ":"
-                    + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
-          }
-          setChainMenuItems(chains);
-
-          colourBySequence(ap);
-
-          StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
-                  + pdbentry.getId());
+    setChainMenuItems(jmb.chainNames);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
 
-          if (pdbentry.getProperty() != null)
-          {
-            if (pdbentry.getProperty().get("method") != null)
-            {
-              title.append(" Method: ");
-              title.append(pdbentry.getProperty().get("method"));
-            }
-            if (pdbentry.getProperty().get("chains") != null)
-            {
-              title.append(" Chain:");
-              title.append(pdbentry.getProperty().get("chains"));
-            }
-          }
-
-          this.setTitle(title.toString());
-
-        }
-        else
-        {
-          // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
-          // and try to find a home - either on a matching sequence or as a new sequence.
-          String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-                  "PDB");
-          // parse pdb file into a chain, etc.
-          // locate best match for pdb in associated views and add mapping to
-          // ssm
-          modelsloaded=true;
-        }
-      }
-      }
-      if (modelsloaded) {
-      // FILE LOADED OK
-      jmolpopup.updateComputedMenus();
-      viewer
-              .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-
-      ssm.addStructureViewerListener(this);
-    }
-  }
-
-  public void sendConsoleEcho(String strEcho)
-  {
-    if (scriptWindow == null)
-      showConsole(true);
-
-    history.append("\n" + strEcho);
-  }
-
-  public void sendConsoleMessage(String strStatus)
-  {
-    if (history != null && strStatus != null
-            && !strStatus.equals("Script completed"))
-    {
-      history.append("\n" + strStatus);
-    }
-  }
-
-  public void notifyScriptTermination(String strStatus, int msWalltime)
-  {
-  }
-
-  public void handlePopupMenu(int x, int y)
-  {
-    jmolpopup.show(x, y);
-  }
-
-  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
-  {
-    notifyAtomPicked(iatom, strMeasure, null);
-  }
-
-  public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
-  {
-    if (strData != null)
-    {
-      System.err.println("Ignoring additional pick data string " + strData);
-    }
-    int chainSeparator = strInfo.indexOf(":");
-    int p=0;
-    if (chainSeparator == -1)
-      chainSeparator = strInfo.indexOf(".");
-
-    String picked = strInfo.substring(strInfo.indexOf("]") + 1,
-            chainSeparator);
-    String mdlString="";
-    if ((p=strInfo.indexOf(":")) > -1)
-      picked += strInfo.substring(p + 1, strInfo
-              .indexOf("."));
-
-    if ((p=strInfo.indexOf("/"))> -1)
-            {
-      mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
-            }
-    picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
-    jmolHistory(false);
-
-    if (!atomsPicked.contains(picked))
-    {
-      viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
-      atomsPicked.addElement(picked);
-    }
-    else
-    {
-      viewer.evalString("select " + picked + ";label off");
-      atomsPicked.removeElement(picked);
-    }
-    jmolHistory(true);
-
-  }
-
-  public void notifyAtomHovered(int atomIndex, String strInfo, String data)
-  {
-    if (data != null)
-    {
-      System.err.println("Ignoring additional hover info: " + data);
-    }
-    mouseOverStructure(atomIndex, strInfo);
+    setTitle(jmb.getViewerTitle());
   }
 
   public void showUrl(String url)
@@ -1047,7 +541,7 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       currentSize = this.getSize();
       rectClip = g.getClipBounds();
 
-      if (viewer == null)
+      if (jmb.viewer == null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
@@ -1057,102 +551,41 @@ public class AppletJmol extends EmbmenuFrame implements StructureListener,
       }
       else
       {
-        viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
       }
     }
   }
-
-  public String createImage(String fileName, String type,
-          Object textOrBytes, int quality)
+/*
+  @Override
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbId)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return jmb.getColour(atomIndex, pdbResNum, chain, pdbId);
   }
 
-  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
+  @Override
+  public String[] getPdbFile()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return jmb.getPdbFile();
   }
 
-  public Hashtable getRegistryInfo()
+  @Override
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbId)
   {
-    // TODO Auto-generated method stub
-    return null;
-  }
+    jmb.highlightAtom(atomIndex, pdbResNum, chain, pdbId);
 
-  public void notifyCallback(int type, Object[] data)
-  {
-    try
-    {
-      switch (type)
-      {
-      case JmolConstants.CALLBACK_LOADSTRUCT:
-        notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4], ((Integer) data[5])
-                        .intValue());
-
-        break;
-      case JmolConstants.CALLBACK_PICK:
-        notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
-        // also highlight in alignment
-      case JmolConstants.CALLBACK_HOVER:
-        notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
-        break;
-      case JmolConstants.CALLBACK_SCRIPT:
-        notifyScriptTermination((String) data[2], ((Integer) data[3])
-                .intValue());
-        break;
-      case JmolConstants.CALLBACK_ECHO:
-        sendConsoleEcho((String) data[1]);
-        break;
-      case JmolConstants.CALLBACK_MESSAGE:
-        sendConsoleMessage((data == null) ? ((String) null)
-                : (String) data[1]);
-        break;
-      case JmolConstants.CALLBACK_MEASURE:
-      case JmolConstants.CALLBACK_CLICK:
-      default:
-        System.err.println("Unhandled callback " + type + " " + data);
-        break;
-      }
-    } catch (Exception e)
-    {
-      System.err.println("Squashed Jmol callback handler error:");
-      e.printStackTrace();
-    }
   }
 
-  public boolean notifyEnabled(int callbackPick)
+  @Override
+  public void mouseOverStructure(int atomIndex, String strInfo)
   {
-    switch (callbackPick)
-    {
-    case JmolConstants.CALLBACK_ECHO:
-    case JmolConstants.CALLBACK_LOADSTRUCT:
-    case JmolConstants.CALLBACK_MEASURE:
-    case JmolConstants.CALLBACK_MESSAGE:
-    case JmolConstants.CALLBACK_PICK:
-    case JmolConstants.CALLBACK_SCRIPT:
-    case JmolConstants.CALLBACK_HOVER:
-    case JmolConstants.CALLBACK_ERROR:
-      return true;
-    case JmolConstants.CALLBACK_CLICK:
-    case JmolConstants.CALLBACK_ANIMFRAME:
-    case JmolConstants.CALLBACK_MINIMIZATION:
-    case JmolConstants.CALLBACK_RESIZE:
-    case JmolConstants.CALLBACK_SYNC:
-    }
-    return false;
-  }
+    jmb.mouseOverStructure(atomIndex, strInfo);
 
-  public void setCallbackFunction(String callbackType,
-          String callbackFunction)
+  }
+*/
+  public void setJalviewColourScheme(UserColourScheme ucs)
   {
-    System.err.println("Ignoring set-callback request to associate "
-            + callbackType + " with function " + callbackFunction);
-
+    jmb.setJalviewColourScheme(ucs);
   }
-
 }
diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
new file mode 100644
index 0000000..745e8f7
--- /dev/null
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -0,0 +1,107 @@
+/**
+ * 
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
+import org.jmol.popup.JmolPopup;
+
+class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+{
+
+  /**
+   * 
+   */
+  private AppletJmol appletJmolBinding;
+
+  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[] seq,
+          String[] chains, String protocol)
+  {
+    super(pdbentry, seq, chains, protocol);
+    appletJmolBinding = appletJmol;
+  }
+
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer()
+  {
+    if (appletJmolBinding.ap.av.showSequenceFeatures)
+    {
+      if (appletJmolBinding.fr == null)
+      {
+        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
+      }
+
+      appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
+    }
+
+    return appletJmolBinding.fr;
+  }
+
+  @Override
+  public jalview.api.SequenceRenderer getSequenceRenderer()
+  {
+    return new SequenceRenderer(appletJmolBinding.ap.av);
+  }
+
+  public void sendConsoleEcho(String strEcho)
+  {
+    if (appletJmolBinding.scriptWindow == null)
+      appletJmolBinding.showConsole(true);
+
+    appletJmolBinding.history.append("\n" + strEcho);
+  }
+
+  public void sendConsoleMessage(String strStatus)
+  {
+    if (appletJmolBinding.history != null && strStatus != null
+            && !strStatus.equals("Script completed"))
+    {
+      appletJmolBinding.history.append("\n" + strStatus);
+    }
+  }
+
+  @Override
+  public void showUrl(String url, String target)
+  {
+    appletJmolBinding.ap.alignFrame.showURL(url, target);
+
+  }
+
+  @Override
+  public void updateUI()
+  {
+    appletJmolBinding.updateTitleAndMenus();
+  }
+  
+  public void updateColours(Object source)
+  {
+    AlignmentPanel ap = (AlignmentPanel) source;
+    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+  }
+
+  public void showUrl(String url)
+  {
+    try
+    {
+      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
+              "jmol");
+    } catch (java.net.MalformedURLException ex)
+    {
+    }
+  }
+
+  public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
+  {
+    
+    jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
+  }
+
+  @Override
+  public void notifyScriptTermination(String strStatus, int msWalltime)
+  {
+    // do nothing.
+  }
+
+}
\ No newline at end of file
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index fbd7176..af83e48 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -17,6 +17,8 @@
  */
 package jalview.ext.jmol;
 
+import java.io.File;
+import java.net.URL;
 import java.util.*;
 import java.awt.*;
 import java.awt.event.*;
@@ -40,6 +42,26 @@ public abstract class JalviewJmolBinding implements StructureListener,
         JmolStatusListener, SequenceStructureBinding
 
 {
+  /**
+   * set if Jmol state is being restored from some source - instructs binding
+   * not to apply default display style when structure set is updated for first
+   * time.
+   */
+  private boolean loadingFromArchive = false;
+  /**
+   * state flag used to check if the Jmol viewer's paint method can be called
+   */
+  private boolean finishedInit=false;
+  
+  public boolean isFinishedInit()
+  {
+    return finishedInit;
+  }
+
+  public void setFinishedInit(boolean finishedInit)
+  {
+    this.finishedInit = finishedInit;
+  }
 
   boolean allChainsSelected = false;
 
@@ -51,7 +73,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   Vector atomsPicked = new Vector();
 
-  private Vector chainNames;
+  public Vector chainNames;
 
   String[] chains;
 
@@ -59,7 +81,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   StringBuffer eval = new StringBuffer();
 
-  String fileLoadingError;
+  public String fileLoadingError;
 
   /**
    * the default or current model displayed if the model cannot be identified
@@ -67,7 +89,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   int frameNo = 0;
 
-  JmolPopup jmolpopup;
+  protected JmolPopup jmolpopup;
 
   String lastCommand;
 
@@ -80,7 +102,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   String[] modelFileNames = null;
 
-  PDBEntry[] pdbentry;
+  public PDBEntry[] pdbentry;
 
   /**
    * datasource protocol for access to PDBEntry
@@ -89,15 +111,20 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   StringBuffer resetLastRes = new StringBuffer();
 
-  SequenceI[] sequence;
+  public SequenceI[] sequence;
 
   StructureSelectionManager ssm;
 
-  JmolViewer viewer;
+  public JmolViewer viewer;
 
   public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
           String[] chains, String protocol)
   {
+    this.sequence = seq;
+    this.chains = chains;
+    this.pdbentry = pdbentry;
+    this.protocol = protocol;
+
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -108,13 +135,41 @@ public abstract class JalviewJmolBinding implements StructureListener,
   }
 
   /**
+   * construct a title string for the viewer window based on the data jalview knows about
+   * @return 
+   */
+  public String getViewerTitle() {
+    if (sequence==null || pdbentry==null || sequence.length<1 || pdbentry.length<1)
+    {
+      return("Jalview Jmol Window");
+    }
+    StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+            + pdbentry[0].getId());
+
+    if (pdbentry[0].getProperty() != null)
+    {
+      if (pdbentry[0].getProperty().get("method") != null)
+      {
+        title.append(" Method: ");
+        title.append(pdbentry[0].getProperty().get("method"));
+      }
+      if (pdbentry[0].getProperty().get("chains") != null)
+      {
+        title.append(" Chain:");
+        title.append(pdbentry[0].getProperty().get("chains"));
+      }
+    }
+    return title.toString();
+  }
+
+  /**
    * prepare the view for a given set of models/chains. chainList contains
    * strings of the form 'pdbfilename:Chaincode'
    * 
    * @param chainList
    *          list of chains to make visible
    */
-  void centerViewer(Vector chainList)
+  public void centerViewer(Vector chainList)
   {
     StringBuffer cmd = new StringBuffer();
     String lbl;
@@ -133,15 +188,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
     }
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
-
-    jmolHistory(false);
-    viewer
-            .evalString("select *;restrict " + cmd + ";cartoon;center "
+    evalStateCommand("select *;restrict " + cmd + ";cartoon;center "
                     + cmd);
-    jmolHistory(true);
   }
 
-  void closeViewer()
+  public void closeViewer()
   {
     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
     // remove listeners for all structures in viewer
@@ -150,28 +201,109 @@ public abstract class JalviewJmolBinding implements StructureListener,
     // and shut down jmol
     viewer.evalStringQuiet("zap");
     viewer.setJmolStatusListener(null);
-
+    lastCommand=null;
     viewer = null;
   }
 
   public void colourByChain()
   {
-    jmolHistory(false);
     colourBySequence = false;
-    viewer.evalStringQuiet("select *;color chain");
-    jmolHistory(true);
-  } 
+    evalStateCommand("select *;color chain");
+  }
 
   public void colourByCharge()
   {
-    jmolHistory(false);
     colourBySequence = false;
-    viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
+    evalStateCommand("select *;color white;select ASP,GLU;color red;"
             + "select LYS,ARG;color blue;select CYS;color yellow");
-    jmolHistory(true);
   }
 
   /**
+   * superpose the structures associated with sequences in the alignment
+   * according to their corresponding positions.
+   */
+  public void superposeStructures(AlignmentI alignment)
+  {
+    String[] files = getPdbFile();
+
+    StringBuffer command = new StringBuffer();
+    boolean matched[] = new boolean[alignment.getWidth()];
+    String commonpositions[][] = new String[files.length][alignment
+            .getWidth()];
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    {
+      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+      if (mapping == null || mapping.length < 1)
+        continue;
+
+      int lastPos = -1;
+      for (int s = 0; s < sequence.length; s++)
+      {
+        for (int sp, m = 0; m < mapping.length; m++)
+        {
+          if (mapping[m].getSequence() == sequence[s]
+                  && (sp = alignment.findIndex(sequence[s])) > -1)
+          {
+            SequenceI asp = alignment.getSequenceAt(sp);
+            for (int r = 0; r < asp.getLength(); r++)
+            {
+              // no mapping to gaps in sequence
+              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+              {
+                matched[r] = false; // exclude from common set
+                continue;
+              }
+              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+              if (pos < 1 || pos == lastPos)
+                continue;
+
+              lastPos = pos;
+
+              commonpositions[m][r] = (mapping[m].getChain() != " " ? ":"
+                      + mapping[m].getChain() : "")
+                      + "/" + (pdbfnum + 1) + ".1";
+            }
+            break;
+          }
+        }
+      }
+    }
+    command.append("select ");
+    // form the matched pair selection strings
+    String sep = "";
+    for (int r = 0; r < matched.length; r++)
+    {
+      if (matched[r])
+      {
+        command.append(sep);
+        command.append("(");
+        for (int s = 0; s < commonpositions.length; s++)
+        {
+          if (s > 0)
+          {
+            command.append(" | ");
+          }
+          command.append(commonpositions[s][r]);
+        }
+        command.append(")");
+        sep = " | ";
+      }
+    }
+    evalStateCommand(command.toString());
+  }
+
+  public void evalStateCommand(String command) {
+    jmolHistory(false);
+    if (lastCommand == null || !lastCommand.equals(command))
+    {
+      viewer.evalStringQuiet(command+"\n");
+    }
+    jmolHistory(true);
+    lastCommand = command;
+  }
+  /**
    * colour any structures associated with sequences in the given alignment
    * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
    * if colourBySequence is enabled.
@@ -180,6 +312,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (!colourBySequence)
       return;
+    if (ssm==null)
+    {
+      return;
+    }
     String[] files = getPdbFile();
     SequenceRenderer sr = getSequenceRenderer();
 
@@ -252,14 +388,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
         }
       }
     }
+    evalStateCommand(command.toString());
+  }
 
-    jmolHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command.toString()))
-    {
-      viewer.evalStringQuiet(command.toString());
-    }
-    jmolHistory(true);
-    lastCommand = command.toString();
+  public boolean isColourBySequence()
+  {
+    return colourBySequence;
+  }
+
+  public void setColourBySequence(boolean colourBySequence)
+  {
+    this.colourBySequence = colourBySequence;
   }
 
   StringBuffer condenseCommand(String command, int pos)
@@ -288,12 +427,13 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   public void createImage(String file, String type, int quality)
   {
+    System.out.println("JMOL CREATE IMAGE");
   }
 
   public String createImage(String fileName, String type,
           Object textOrBytes, int quality)
   {
-    // TODO Auto-generated method stub
+    System.out.println("JMOL CREATE IMAGE");
     return null;
   }
 
@@ -333,7 +473,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * 
    * @return
    */
-  abstract FeatureRenderer getFeatureRenderer();
+  public abstract FeatureRenderer getFeatureRenderer();
 
   private int getModelNum(String modelFileName)
   {
@@ -378,7 +518,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * 
    * @return
    */
-  abstract SequenceRenderer getSequenceRenderer();
+  public abstract SequenceRenderer getSequenceRenderer();
 
   // ///////////////////////////////
   // JmolStatusListener
@@ -449,9 +589,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   }
 
+  boolean debug = true;
+
   private void jmolHistory(boolean enable)
   {
-    viewer.setBooleanProperty("history", enable);
+    viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
   }
 
   public void loadInline(String string)
@@ -518,7 +660,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (data != null)
     {
-      System.err.println("Ignoring additional hover info: " + data);
+      System.err.println("Ignoring additional hover info: " + data+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
   }
@@ -569,6 +711,14 @@ public abstract class JalviewJmolBinding implements StructureListener,
       atomsPicked.removeElement(picked);
     }
     jmolHistory(true);
+    // TODO: in application this happens
+    //
+//if (scriptWindow != null)
+//    {
+//      scriptWindow.sendConsoleMessage(strInfo);
+//      scriptWindow.sendConsoleMessage("\n");
+//    }
+
 
   }
 
@@ -603,10 +753,19 @@ public abstract class JalviewJmolBinding implements StructureListener,
         sendConsoleMessage((data == null) ? ((String) null)
                 : (String) data[1]);
         break;
+      case JmolConstants.CALLBACK_ERROR:
+        // System.err.println("Ignoring error callback.");
+        break;
+      case JmolConstants.CALLBACK_SYNC:
+      case JmolConstants.CALLBACK_RESIZE:
+        updateUI();
+        break;
       case JmolConstants.CALLBACK_MEASURE:
+        
       case JmolConstants.CALLBACK_CLICK:
+        
       default:
-        System.err.println("Unhandled callback " + type + " " + data);
+        System.err.println("Unhandled callback " + type + " " + data[1].toString());
         break;
       }
     } catch (Exception e)
@@ -629,11 +788,11 @@ public abstract class JalviewJmolBinding implements StructureListener,
     case JmolConstants.CALLBACK_HOVER:
     case JmolConstants.CALLBACK_ERROR:
       return true;
+    case JmolConstants.CALLBACK_RESIZE:
+    case JmolConstants.CALLBACK_SYNC:
     case JmolConstants.CALLBACK_CLICK:
     case JmolConstants.CALLBACK_ANIMFRAME:
     case JmolConstants.CALLBACK_MINIMIZATION:
-    case JmolConstants.CALLBACK_RESIZE:
-    case JmolConstants.CALLBACK_SYNC:
     }
     return false;
   }
@@ -648,11 +807,46 @@ public abstract class JalviewJmolBinding implements StructureListener,
       return;
     }
     fileLoadingError = null;
+    String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
     ssm = StructureSelectionManager.getStructureSelectionManager();
+    // first check if we've lost any structures
+    if (oldmodels!=null && oldmodels.length>0)
+    {
+      int oldm=0;
+      for (int i=0;i<oldmodels.length;i++)
+      {
+        for (int n=0;n<modelfilenames.length; n++)
+        {
+          if (modelfilenames[n]==oldmodels[i])
+          {
+            oldmodels[i]=null;
+            break;
+          }
+        }
+        if (oldmodels[i]!=null)
+        {
+          oldm++;
+        }
+      }
+      if (oldm>0)
+      {
+        String[] oldmfn = new String[oldm];
+        oldm=0;
+        for (int i=0;i<oldmodels.length; i++)
+        {
+          if (oldmodels[i]!=null) {
+            oldmfn[oldm++] = oldmodels[i];
+          }
+        }
+        // deregister the Jmol instance for these structures - we'll add 
+        // ourselves again at the end for the current structure set. 
+        ssm.removeStructureViewerListener(this, oldmfn);
+      }
+    }
     for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
     {
       String fileName = modelfilenames[modelnum];
@@ -683,9 +877,22 @@ public abstract class JalviewJmolBinding implements StructureListener,
                 // needs
                 // to be tested. See mantis bug
                 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-
+                String protocol = AppletFormatAdapter.URL;
+                try
+                {
+                  File fl = new java.io.File(pdbentry[pe].getFile());
+                  if (fl.exists())
+                  {
+                    protocol = AppletFormatAdapter.FILE;
+                  }
+                } catch (Exception e)
+                {
+                } catch (Error e)
+                {
+                }
+                ;
                 pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
-                        .getFile(), AppletFormatAdapter.URL);
+                        .getFile(), protocol);
 
               }
 
@@ -712,7 +919,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
             // parse pdb file into a chain, etc.
             // locate best match for pdb in associated views and add mapping to
             // ssm
-            // if properly registered then notifyLoaded=true;
+            // if properly registered then
+            notifyLoaded = true;
           }
         }
       }
@@ -720,16 +928,24 @@ public abstract class JalviewJmolBinding implements StructureListener,
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
     jmolpopup.updateComputedMenus();
-    viewer
-            .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+    if (!isLoadingFromArchive())
+    {
+      viewer
+              .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+    }
+    setLoadingFromArchive(false);
     // register ourselves as a listener and notify the gui that it needs to
     // update itself.
     ssm.addStructureViewerListener(this);
     if (notifyLoaded)
     {
+      FeatureRenderer fr = getFeatureRenderer();
+      if (fr!=null)
+      {
+        fr.featuresAdded();
+      }
       updateUI();
     }
-
   }
 
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
@@ -737,9 +953,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     notifyAtomPicked(iatom, strMeasure, null);
   }
 
-  public void notifyScriptTermination(String strStatus, int msWalltime)
-  {
-  }
+  public abstract void notifyScriptTermination(String strStatus, int msWalltime);
 
   /**
    * display a message echoed from the jmol viewer
@@ -782,7 +996,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     int index;
     Color col;
     jmolHistory(false);
-
+    // TODO: Switch between nucleotide or aa selection expressions
     Enumeration en = ResidueProperties.aa3Hash.keys();
     StringBuffer command = new StringBuffer("select *;color white;");
     while (en.hasMoreElements())
@@ -798,7 +1012,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
               + col.getGreen() + "," + col.getBlue() + "];");
     }
 
-    viewer.evalStringQuiet(command.toString());
+    evalStateCommand(command.toString());
     jmolHistory(true);
   }
 
@@ -819,6 +1033,30 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * state change. this could be because structures were loaded, or because an
    * error has occured.
    */
-  abstract void updateUI();
+  public abstract void updateUI();
+
+  public void allocateViewer(Component renderPanel, String htmlName,
+          URL documentBase, URL codeBase, String commandOptions)
+  {
+    viewer = JmolViewer.allocateViewer(renderPanel,
+            new SmarterJmolAdapter(), htmlName+((Object) this).toString(), documentBase, codeBase,
+            commandOptions, this);
+  }
 
+  public void setLoadingFromArchive(boolean loadingFromArchive)
+  {
+    this.loadingFromArchive = loadingFromArchive;
+  }
+
+  public boolean isLoadingFromArchive()
+  {
+    return loadingFromArchive;
+  }
+  public void setBackgroundColour(java.awt.Color col)
+  {
+    jmolHistory(false);
+    viewer.evalStringQuiet("background [" + col.getRed() + ","
+            + col.getGreen() + "," + col.getBlue() + "];");
+    jmolHistory(true);
+  }
 }
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index dcca874..e274b84 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -41,36 +41,20 @@ import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 
-public class AppJmol extends GStructureViewer implements StructureListener,
-        JmolStatusListener, Runnable, SequenceStructureBinding
+public class AppJmol extends GStructureViewer implements Runnable,
+        SequenceStructureBinding
 
 {
-  JmolViewer viewer;
-
-  JmolPopup jmolpopup;
+  AppJmolBinding jmb;
 
   ScriptWindow scriptWindow;
 
-  PDBEntry pdbentry;
-
-  SequenceI[] sequence;
-
-  String[] chains;
-
-  StructureSelectionManager ssm;
-
   JSplitPane splitPane;
 
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
 
-  String fileLoadingError;
-
-  boolean colourBySequence = true;
-
-  boolean loadingFromArchive = false;
-
   Vector atomsPicked = new Vector();
 
   public AppJmol(String file, String id, SequenceI[] seq,
@@ -83,21 +67,23 @@ public class AppJmol extends GStructureViewer implements StructureListener,
           AlignmentPanel ap, String loadStatus, Rectangle bounds,
           String viewid)
   {
-    loadingFromArchive = true;
-    pdbentry = new PDBEntry();
+    PDBEntry pdbentry = new PDBEntry();
     pdbentry.setFile(file);
     pdbentry.setId(id);
-    this.sequence = seq;
+    // / TODO: check if protocol is needed to be set, and if chains are
+    // autodiscovered.
+    jmb = new AppJmolBinding(this, new PDBEntry[]
+    { pdbentry }, seq, null, null);
+
+    jmb.setLoadingFromArchive(true);
     this.ap = ap;
     this.setBounds(bounds);
-    colourBySequence = false;
+    jmb.setColourBySequence(false);
     seqColour.setSelected(false);
     viewId = viewid;
     // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
     // bounds.width,bounds.height);
 
-    initJmol(loadStatus);
-
     this.addInternalFrameListener(new InternalFrameAdapter()
     {
       public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
@@ -105,21 +91,8 @@ public class AppJmol extends GStructureViewer implements StructureListener,
         closeViewer();
       }
     });
-  }
+    initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
 
-  public synchronized void addSequence(SequenceI[] seq)
-  {
-    Vector v = new Vector();
-    for (int i = 0; i < sequence.length; i++)
-      v.addElement(sequence[i]);
-
-    for (int i = 0; i < seq.length; i++)
-      if (!v.contains(seq[i]))
-        v.addElement(seq[i]);
-
-    SequenceI[] tmp = new SequenceI[v.size()];
-    v.copyInto(tmp);
-    sequence = tmp;
   }
 
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
@@ -138,7 +111,7 @@ public class AppJmol extends GStructureViewer implements StructureListener,
                       Desktop.desktop,
                       pdbentry.getId()
                               + " is already displayed."
-                              + "\nDo you want to map sequences to the visible structure?",
+                              + "\nDo you want to re-use this viewer ?",
                       "Map Sequences to Visible Window: "
                               + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
 
@@ -162,10 +135,15 @@ public class AppJmol extends GStructureViewer implements StructureListener,
           if (frames[i] instanceof AppJmol)
           {
             AppJmol topJmol = ((AppJmol) frames[i]);
-            if (topJmol.pdbentry.getFile().equals(alreadyMapped))
+            // JBPNOTE: this looks like a binding routine, rather than a gui
+            // routine
+            for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
             {
-              topJmol.addSequence(seq);
-              break;
+              if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
+              {
+                topJmol.jmb.addSequence(seq);
+                break;
+              }
             }
           }
         }
@@ -175,13 +153,10 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     }
     // /////////////////////////////////
 
+    jmb = new AppJmolBinding(this, new PDBEntry[]
+    { pdbentry }, seq, null, null);
     this.ap = ap;
-    this.pdbentry = pdbentry;
-    this.sequence = seq;
-    this.setSize(400, 400);
-    // jalview.gui.Desktop.addInternalFrame(this, "Jmol
-    // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId()
-    // : ""), 400, 400);
+    setSize(400, 400); // probably should be a configurable/dynamic default here
 
     if (pdbentry.getFile() != null)
     {
@@ -200,49 +175,31 @@ public class AppJmol extends GStructureViewer implements StructureListener,
         closeViewer();
       }
     });
+
   }
 
   void initJmol(String command)
   {
+    jmb.setFinishedInit(false);
     renderPanel = new RenderPanel();
-
+    // TODO: consider waiting until the structure/view is fully loaded before
+    // displaying
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-
-    StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
-            + pdbentry.getId());
-
-    if (pdbentry.getProperty() != null)
-    {
-      if (pdbentry.getProperty().get("method") != null)
-      {
-        title.append(" Method: ");
-        title.append(pdbentry.getProperty().get("method"));
-      }
-      if (pdbentry.getProperty().get("chains") != null)
-      {
-        title.append(" Chain:");
-        title.append(pdbentry.getProperty().get("chains"));
-      }
-    }
-
-    this.setTitle(title.toString());
-    jalview.gui.Desktop.addInternalFrame(this, title.toString(),
+    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);
-    // * OK, but safer to assign htmlName, URL bases, comandOptions, and
-    // statusListener now.
-
-    viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel,
-            new SmarterJmolAdapter(), "", null, null, "", this);
-
-    jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
-
-    viewer.evalStringQuiet(command);
+    jmb.allocateViewer(renderPanel, "", null, null, "");
+    jmb.newJmolPopup(true, "Jmol", true);
+    jmb.evalStateCommand(command);
+    jmb.setFinishedInit(true);
   }
 
   void setChainMenuItems(Vector chains)
   {
     chainMenu.removeAll();
-
+    if (chains==null)
+    {
+      return;
+    }
     JMenuItem menuItem = new JMenuItem("All");
     menuItem.addActionListener(new ActionListener()
     {
@@ -281,101 +238,90 @@ public class AppJmol extends GStructureViewer implements StructureListener,
 
   void centerViewer()
   {
-    jmolHistory(false);
-    StringBuffer cmd = new StringBuffer();
+    Vector toshow = new Vector();
     String lbl;
-    int mlength, p,mnum;
+    int mlength, p, mnum;
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
       {
         JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
         if (item.isSelected())
-        {          lbl = item.getText();
-        mlength = 0;
-        do
-        {
-          p = mlength;
-          mlength = lbl.indexOf(":", p);
-        } while (p < mlength && mlength < (lbl.length() - 2));
-        if (pdbentry.getId().equals(lbl.substring(0,mlength)))
         {
-          mnum = 1+getModelNum(pdbentry.getFile());
-        if (mnum>0)
-          {cmd.append(":" + lbl.substring(mlength + 1) + " /"
-                + mnum + " or ");
-          }
-        }
+          toshow.addElement(item.getText());
         }
       }
     }
-
-    if (cmd.length() > 0)
-      cmd.setLength(cmd.length() - 4);
-
-    viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center "
-            + cmd);
-    jmolHistory(true);
-  }
-  private int getModelNum(String modelFileName)
-  {
-    String[] mfn = getPdbFile();
-    if (mfn == null)
-    {
-      return -1;
-    }
-    for (int i = 0; i < mfn.length; i++)
-    {
-      if (mfn[i].equalsIgnoreCase(modelFileName))
-        return i;
-    }
-    return -1;
+    jmb.centerViewer(toshow);
   }
 
   void closeViewer()
   {
-    viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
-    // remove listeners for all structures in viewer
-    StructureSelectionManager.getStructureSelectionManager()
-            .removeStructureViewerListener(this, getPdbFile());
-    // and shut down jmol
-    viewer.evalStringQuiet("zap");
-    viewer.setJmolStatusListener(null);
-    viewer = null;
+    jmb.closeViewer();
+    // TODO: check for memory leaks where instance isn't finalised because jmb
+    // holds a reference to the window
+    jmb = null;
   }
 
   public void run()
   {
+    String pdbid = "";
+    // todo - record which pdbids were successfuly imported.
+    StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
     try
     {
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
       jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
-      AlignmentI pdbseq;
-      if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null)
-      {
-        // just transfer the file name from the first seuqence's first PDBEntry
-        pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
-                .elementAt(0)).getFile());
-        initJmol("load " + pdbentry.getFile());
-      }
-      else
+      for (int pi = 0; pi < jmb.pdbentry.length; pi++)
       {
-        JOptionPane
-                .showInternalMessageDialog(
-                        Desktop.desktop,
-                        pdbentry.getId()
-                                + " could not be retrieved. Please try downloading the file manually.",
-                        "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
+        AlignmentI pdbseq;
+        if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
+                .getId())) != null)
+        {
+          String file;
+          // just transfer the file name from the first sequence's first
+          // PDBEntry
+          jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq.getSequenceAt(
+                  0).getPDBId().elementAt(0)).getFile());
+          files.append("\"" + file + "\"");
+        }
+        else
+        {
+          errormsgs.append("'" + pdbid + "' ");
+        }
       }
     } catch (OutOfMemoryError oomerror)
     {
-      new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD",
-              oomerror);
+      new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
     } catch (Exception ex)
     {
       ex.printStackTrace();
+      errormsgs.append("'" + pdbid + "'");
+    }
+    if (errormsgs.length() > 0)
+    {
+
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "The following pdb entries could not be retrieved from the PDB:\n"
+                      + errormsgs.toString()
+                      + "\nPlease try downloading them manually.",
+              "Couldn't load file", JOptionPane.ERROR_MESSAGE);
+
+    }
+    if (files.length() > 0)
+    {
+      try
+      {
+        initJmol("load FILES " + files.toString());
+      } catch (OutOfMemoryError oomerror)
+      {
+        new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+        Cache.log.debug("File locations are " + files);
+      } catch (Exception ex)
+      {
+        Cache.log.error("Couldn't open Jmol viewer!", ex);
+      }
     }
   }
 
@@ -394,8 +340,8 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     {
       try
       {
-        BufferedReader in = new BufferedReader(new FileReader(pdbentry
-                .getFile()));
+        // TODO: cope with multiple PDB files in view 
+        BufferedReader in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
         File outFile = chooser.getSelectedFile();
 
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -420,8 +366,11 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
     jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
             550, 600);
-    cap.setText(StructureSelectionManager.getStructureSelectionManager()
-            .printMapping(pdbentry.getFile()));
+    for (int pdbe = 0; pdbe<jmb.pdbentry.length; pdbe++) {
+      cap.appendText(StructureSelectionManager.getStructureSelectionManager()
+            .printMapping(jmb.pdbentry[pdbe].getFile()));
+      cap.appendText("\n");
+    }
   }
 
   /**
@@ -468,106 +417,76 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     if (im.getGraphics() != null)
     {
       Rectangle rect = new Rectangle(width, height);
-      viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+      jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
       im.writeImage();
     }
   }
 
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
-    lastCommand = null;
-    colourBySequence = seqColour.isSelected();
-    colourBySequence(ap.alignFrame.alignPanel);
+    jmb.setColourBySequence(seqColour.isSelected());
+    // Set the colour using the current view for the associated alignframe
+    jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures, ap.alignFrame.viewport.alignment);
   }
 
   public void chainColour_actionPerformed(ActionEvent actionEvent)
   {
-    colourBySequence = false;
-    seqColour.setSelected(false);
-    jmolHistory(false);
-    viewer.evalStringQuiet("select *;color chain");
-    jmolHistory(true);
+    chainColour.setSelected(true);
+    jmb.colourByChain();
   }
 
   public void chargeColour_actionPerformed(ActionEvent actionEvent)
   {
-    colourBySequence = false;
-    seqColour.setSelected(false);
-    jmolHistory(false);
-    viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;"
-            + "select LYS,ARG;color blue;select CYS;color yellow");
-    jmolHistory(true);
+    chargeColour.setSelected(true);
+    jmb.colourByCharge();
   }
 
   public void zappoColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new ZappoColourScheme());
+    zappoColour.setSelected(true);
+    jmb.setJalviewColourScheme(new ZappoColourScheme());
   }
 
   public void taylorColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new TaylorColourScheme());
+    taylorColour.setSelected(true);
+    jmb.setJalviewColourScheme(new TaylorColourScheme());
   }
 
   public void hydroColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new HydrophobicColourScheme());
+    hydroColour.setSelected(true);
+    jmb.setJalviewColourScheme(new HydrophobicColourScheme());
   }
 
   public void helixColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new HelixColourScheme());
+    helixColour.setSelected(true);
+    jmb.setJalviewColourScheme(new HelixColourScheme());
   }
 
   public void strandColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new StrandColourScheme());
+    strandColour.setSelected(true);
+    jmb.setJalviewColourScheme(new StrandColourScheme());
   }
 
   public void turnColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new TurnColourScheme());
+    turnColour.setSelected(true);
+    jmb.setJalviewColourScheme(new TurnColourScheme());
   }
 
   public void buriedColour_actionPerformed(ActionEvent actionEvent)
   {
-    setJalviewColourScheme(new BuriedColourScheme());
+    buriedColour.setSelected(true);
+    jmb.setJalviewColourScheme(new BuriedColourScheme());
   }
 
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    jmolHistory(false);
-    colourBySequence = false;
-    seqColour.setSelected(false);
-
-    if (cs == null)
-      return;
-
-    String res;
-    int index;
-    Color col;
-
-    Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
-    while (en.hasMoreElements())
-    {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if (index > 20)
-        continue;
-
-      col = cs.findColour(ResidueProperties.aa[index].charAt(0));
-
-      command.append("select " + res + ";color[" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
-    }
-
-    viewer.evalStringQuiet(command.toString());
-    jmolHistory(true);
-  }
 
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {
+    userColour.setSelected(true);
     new UserDefinedColours(this, null);
   }
 
@@ -575,19 +494,11 @@ public class AppJmol extends GStructureViewer implements StructureListener,
   {
     java.awt.Color col = JColorChooser.showDialog(this,
             "Select Background Colour", null);
-
     if (col != null)
     {
-      jmolHistory(false);
-      viewer.evalStringQuiet("background [" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
-      jmolHistory(true);
+      jmb.setBackgroundColour(col);
     }
   }
-  private void jmolHistory(boolean enable)
-  {
-    viewer.setBooleanProperty("history", enable);
-  }
 
   public void jmolHelp_actionPerformed(ActionEvent actionEvent)
   {
@@ -599,509 +510,6 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     {
     }
   }
-  String[] modelFileNames = null;
-
-  // ////////////////////////////////
-  // /StructureListener
-  public String[] getPdbFile()
-  {
-    if (modelFileNames == null)
-    {
-      String mset[] = new String[viewer.getModelCount()];
-      for (int i = 0; i < mset.length; i++)
-      {
-        try {
-          String mname = viewer.getModelFileName(i);
-          if (mname==null)
-          {
-            System.err.println("Model "+i+" has no filename!");
-            continue;
-          }
-          File fpath = new File(mname);
-          mset[i] = fpath.toString();
-        } catch (Exception e)
-        {
-          System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!");
-        }
-      }
-      modelFileNames = mset;
-    }
-    return modelFileNames;
-  }
-
-  Pattern pattern = Pattern
-          .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?");
-
-  String lastMessage;
-
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    // copied from AppJmol - will be refactored to binding eventually
-    int pdbResNum;
-    int mdlSep = strInfo.indexOf("/");
-    int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
-
-    if (chainSeparator == -1)
-    {
-      chainSeparator = strInfo.indexOf(".");
-      if (mdlSep > -1 && mdlSep < chainSeparator)
-      {
-        chainSeparator1 = chainSeparator;
-        chainSeparator = mdlSep;
-      }
-    }
-    pdbResNum = Integer.parseInt(strInfo.substring(
-            strInfo.indexOf("]") + 1, chainSeparator));
-
-    String chainId;
-
-    if (strInfo.indexOf(":") > -1)
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
-              .indexOf("."));
-    else
-    {
-      chainId = " ";
-    }
-
-    String pdbfilename = pdbentry.getFile();
-    if (mdlSep > -1)
-    {
-      if (chainSeparator1 == -1)
-      {
-        chainSeparator1 = strInfo.indexOf(".", mdlSep);
-      }
-      String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
-              chainSeparator1) : strInfo.substring(mdlSep + 1);
-      try
-      {
-        // recover PDB filename for the model hovered over.
-        pdbfilename = viewer
-                .getModelFileName(new Integer(mdlId).intValue() - 1);
-      } catch (Exception e)
-      {
-      }
-      ;
-    }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
-    lastMessage = strInfo;
-/*
- * Old Implementation based on Pattern regex.
-    Matcher matcher = pattern.matcher(strInfo);
-    matcher.find();
-    matcher.group(1);
-    int pdbResNum = Integer.parseInt(matcher.group(2));
-    String chainId = matcher.group(3);
-    
-    if (chainId != null)
-      chainId = chainId.substring(1, chainId.length());
-    else
-    {
-      chainId = " ";
-    }
-    String mdlId = matcher.group(4);
-    String pdbfilename = pdbentry.getFile();
-
-    if (mdlId!=null && mdlId.length()>0)
-    {
-      try {
-        // recover PDB filename for the model hovered over.
-        pdbfilename = viewer.getModelFileName(new Integer(mdlId).intValue()-1);
-      } catch (Exception e) {};
-    }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-    {
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-    }
-    lastMessage = strInfo; */
-  }
-
-  StringBuffer resetLastRes = new StringBuffer();
-
-  StringBuffer eval = new StringBuffer();
-
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    int mdlNum = 1+getModelNum(pdbfile);
-    if (mdlNum==0)
-    {
-      return;
-    }
-
-    jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
-
-    eval.setLength(0);
-    eval.append("select " + pdbResNum); // +modelNum
-
-    resetLastRes.setLength(0);
-    resetLastRes.append("select " + pdbResNum); // +modelNum
-
-    if (!chain.equals(" "))
-    {
-      eval.append(":");
-      resetLastRes.append(":");
-      eval.append(chain);
-      resetLastRes.append(chain);
-    }
-    // if (mdlNum != 0)
-    {
-      eval.append(" /" + (mdlNum));
-      resetLastRes.append(" /" + (mdlNum));
-    }
-    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
-    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + " and not hetero; spacefill 0;");
-
-    eval.append("spacefill 200;select none");
-
-    viewer.evalStringQuiet(eval.toString());
-    jmolHistory(true);
-  }
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (!pdbfile.equals(pdbentry.getFile()))
-      return null;
-
-    return new Color(viewer.getAtomArgb(atomIndex));
-  }
-
-  public void updateColours(Object source)
-  {
-    colourBySequence((AlignmentPanel) source);
-  }
-
-  // End StructureListener
-  // //////////////////////////
-
-  String lastCommand;
-
-  FeatureRenderer fr = null;
-
-  public void colourBySequence(AlignmentPanel sourceap)
-  {
-    this.ap = sourceap;
-
-    if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av)
-      return;
-
-    String[] files = getPdbFile();
-    
-    SequenceRenderer sr = new SequenceRenderer(ap.av);
-
-    boolean showFeatures = false;
-
-    if (ap.av.showSequenceFeatures)
-    {
-      showFeatures = true;
-      if (fr == null)
-      {
-        fr = new jalview.gui.FeatureRenderer(ap);
-      }
-
-      fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    StringBuffer command = new StringBuffer();
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-    {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
-      if (mapping == null || mapping.length < 1)
-        continue;
-
-
-    int lastPos = -1;
-    for (int sp, s = 0; s < sequence.length; s++)
-    {
-      for (int m = 0; m < mapping.length; m++)
-      {
-        if (mapping[m].getSequence() == sequence[s]
-                && (sp = ap.av.alignment.findIndex(sequence[s])) > -1)
-        {
-          SequenceI asp = ap.av.alignment.getSequenceAt(sp);
-          for (int r = 0; r < asp.getLength(); r++)
-          {
-            // No mapping to gaps in sequence.
-            if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
-            {
-              continue;
-            }
-            int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
-            if (pos < 1 || pos == lastPos)
-              continue;
-
-            lastPos = pos;
-
-            Color col = sr.getResidueBoxColour(asp, r);
-
-            if (showFeatures)
-              col = fr.findFeatureColour(col, asp, r);
-            String newSelcom = (mapping[m].getChain() != " " ? ":"
-                    + mapping[m].getChain() : "")
-                    + "/"
-                    + (pdbfnum + 1)
-                    + ".1"
-                    + ";color["
-                    + col.getRed()
-                    + ","
-                    + col.getGreen()
-                    + ","
-                    + col.getBlue() + "]";
-            if (command.toString().endsWith(newSelcom))
-            {
-              command = condenseCommand(command, pos);
-              continue;
-            }
-
-            command.append(";select " + pos);
-            command.append(newSelcom);
-          }
-          break;
-        }
-      }
-      }
-    }
-    jmolHistory(false);
-
-    if (lastCommand == null || !lastCommand.equals(command.toString()))
-    {
-      viewer.evalStringQuiet(command.toString());
-    }
-    jmolHistory(true);
-    lastCommand = command.toString();
-  }
-
-  StringBuffer condenseCommand(StringBuffer command, int pos)
-  {
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
-
-    command.delete(0, sb.length());
-
-    String start;
-
-    if (command.indexOf("-") > -1)
-    {
-      start = command.substring(0, command.indexOf("-"));
-    }
-    else
-    {
-      start = command.substring(0, command.indexOf(":"));
-    }
-
-    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
-    return sb;
-  }
-
-  // ///////////////////////////////
-  // JmolStatusListener
-
-  public String eval(String strEval)
-  {
-    // System.out.println(strEval);
-    // "# 'eval' is implemented only for the applet.";
-    return null;
-  }
-
-  public void createImage(String file, String type, int quality)
-  {
-    System.out.println("JMOL CREATE IMAGE");
-  }
-
-  public void notifyFileLoaded(String fullPathName, String fileName2,
-          String modelName, String errorMsg, int modelParts)
-  {
-    if (errorMsg != null)
-    {
-      fileLoadingError = errorMsg;
-      repaint();
-      return;
-    }
-
-    fileLoadingError = null;
-    modelFileNames = null;
-    
-    String[] modelfilenames = getPdbFile();
-    ssm = StructureSelectionManager.getStructureSelectionManager();
-    boolean modelsloaded=false;
-    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
-    {
-      String fileName = modelfilenames[modelnum];
-
-    if (fileName != null)
-    {
-      modelsloaded=true;
-      // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename
-      if (pdbentry.getFile().equals(fileName))
-      {
-      // TODO: do some checking using the modelPts number of parts against our
-      // own estimate of the number of chains
-      // FILE LOADED OK
-      MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry
-              .getFile(), AppletFormatAdapter.FILE);
-      Vector chains = new Vector();
-      for (int i = 0; i < pdbFile.chains.size(); i++)
-      {
-        chains
-                .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id));
-      }
-      setChainMenuItems(chains);
-
-      if (!loadingFromArchive)
-      {
-        viewer
-                .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-
-        colourBySequence(ap);
-      }
-      if (fr != null)
-        fr.featuresAdded();
-
-      loadingFromArchive = false;
-    }
-    else {
-      // this is a foreign pdb file that jalview doesn't know about - add it to the dataset
-      // and try to find a home - either on a matching sequence or as a new sequence.
-      String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-              "PDB");
-      // parse pdb file into a chain, etc.
-      // locate best match for pdb in associated views and add mapping to
-      // ssm
-      modelsloaded=true;
-    }
-    }
-    }
-    if (modelsloaded)
-    {
-      ssm.addStructureViewerListener(this);
-      jmolpopup.updateComputedMenus();
-    }
-  }
-
-  public void sendConsoleEcho(String strEcho)
-  {
-    if (scriptWindow != null)
-      scriptWindow.sendConsoleEcho(strEcho);
-  }
-
-  public void sendConsoleMessage(String strStatus)
-  {
-    if (scriptWindow != null)
-      scriptWindow.sendConsoleMessage(strStatus);
-  }
-
-  public void notifyScriptTermination(String strStatus, int msWalltime)
-  {
-    if (scriptWindow != null)
-      scriptWindow.notifyScriptTermination(strStatus, msWalltime);
-  }
-
-  public void handlePopupMenu(int x, int y)
-  {
-    jmolpopup.show(x, y);
-  }
-
-  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
-  {
-    notifyAtomPicked(iatom, strMeasure, null);
-  }
-
-  public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
-  {
-    if (strData != null)
-    {
-      Cache.log.info("Non null pick data string: " + strData
-              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
-    }
-    /*
-    Matcher matcher = pattern.matcher(strInfo);
-    matcher.find();
-
-    matcher.group(1);
-    String resnum = new String(matcher.group(2));
-    String chainId = matcher.group(3);
-
-    String picked = resnum;
-
-
-    if (chainId != null)
-      picked += (":" + chainId.substring(1, chainId.length()));
-*/
-    int chainSeparator = strInfo.indexOf(":");
-    int p=0;
-    if (chainSeparator == -1)
-      chainSeparator = strInfo.indexOf(".");
-
-    String picked = strInfo.substring(strInfo.indexOf("]") + 1,
-            chainSeparator);
-    String mdlString="";
-    if ((p=strInfo.indexOf(":")) > -1)
-      picked += strInfo.substring(p + 1, strInfo
-              .indexOf("."));
-
-    if ((p=strInfo.indexOf("/"))> -1)
-            {
-      mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
-            }
-    picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))";
-    jmolHistory(false);
-    if (!atomsPicked.contains(picked))
-    {
-      // TODO: re-instate chain ID separator dependent labelling for both applet and application
-//      if (chainId != null)
-        viewer.evalString("select " + picked + ";label %n %r:%c");
-//      else
-//        viewer.evalString("select " + picked + ";label %n %r");
-      atomsPicked.addElement(picked);
-    }
-    else
-    {
-      viewer.evalString("select " + picked + ";label off");
-      atomsPicked.removeElement(picked);
-    }
-    jmolHistory(true);
-    if (scriptWindow != null)
-    {
-      scriptWindow.sendConsoleMessage(strInfo);
-      scriptWindow.sendConsoleMessage("\n");
-    }
-  }
-
-  public void notifyAtomHovered(int atomIndex, String strInfo, String data)
-  {
-    if (data != null)
-    {
-      Cache.log.info("Non null hover data string: " + data
-              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
-    }
-    mouseOverStructure(atomIndex, strInfo);
-  }
-
-  @Override
-  public void showUrl(String url)
-  {
-    try
-    {
-      jalview.util.BrowserLauncher.openURL(url);
-    } catch (IOException e)
-    {
-      Cache.log.error("Failed to launch Jmol-associated url " + url, e);
-      // TODO: 2.6 : warn user if browser was not configured.
-    }
-  }
 
   public void showConsole(boolean showConsole)
   {
@@ -1134,14 +542,6 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     validate();
   }
 
-  public float[][] functionXY(String functionName, int x, int y)
-  {
-    return null;
-  }
-
-  // /End JmolStatusListener
-  // /////////////////////////////
-
   class RenderPanel extends JPanel
   {
     final Dimension currentSize = new Dimension();
@@ -1153,26 +553,42 @@ public class AppJmol extends GStructureViewer implements StructureListener,
       getSize(currentSize);
       g.getClipBounds(rectClip);
 
-      if (viewer == null)
-      {
-        g.setColor(Color.black);
-        g.fillRect(0, 0, currentSize.width, currentSize.height);
-        g.setColor(Color.white);
-        g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
-      }
-      else if (fileLoadingError != null)
+      if (jmb.fileLoadingError != null)
       {
         g.setColor(Color.black);
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString("Error loading file..." + pdbentry.getId(), 20,
+        g.drawString("Error loading file...", 20,
                 currentSize.height / 2);
+        StringBuffer sb = new StringBuffer();
+        int lines=0;
+        for (int e=0;e<jmb.pdbentry.length; e++)
+        {
+          sb.append(jmb.pdbentry[e].getId());
+          if (e<jmb.pdbentry.length-1) {
+            sb.append(",");
+          }
+
+          if (e==jmb.pdbentry.length-1 || sb.length()>20)
+          {
+            lines++;
+            g.drawString(sb.toString(), 20, currentSize.height/2 - lines*g.getFontMetrics().getHeight());
+          }
+        }
       }
       else
+        if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
+        {
+          g.setColor(Color.black);
+          g.fillRect(0, 0, currentSize.width, currentSize.height);
+          g.setColor(Color.white);
+          g.setFont(new Font("Verdana", Font.BOLD, 14));
+          g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+        }
+        else 
       {
-        viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
       }
     }
   }
@@ -1187,103 +603,23 @@ public class AppJmol extends GStructureViewer implements StructureListener,
     }
     return viewId;
   }
-
-  @Override
-  public String createImage(String fileName, String type,
-          Object textOrBytes, int quality)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public Hashtable getRegistryInfo()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public void notifyCallback(int type, Object[] data)
+  public void updateTitleAndMenus()
   {
-    try
-    {
-      switch (type)
-      {
-      case JmolConstants.CALLBACK_LOADSTRUCT:
-        notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4], ((Integer) data[5])
-                        .intValue());
-
-        break;
-      case JmolConstants.CALLBACK_PICK:
-        notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
-        // also highlight in alignment
-      case JmolConstants.CALLBACK_HOVER:
-        notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
-        break;
-      case JmolConstants.CALLBACK_SCRIPT:
-        notifyScriptTermination((String) data[2], ((Integer) data[3])
-                .intValue());
-        break;
-      case JmolConstants.CALLBACK_ECHO:
-        sendConsoleEcho((String) data[1]);
-        break;
-      case JmolConstants.CALLBACK_MESSAGE:
-        sendConsoleMessage((data == null) ? ((String) null)
-                : (String) data[1]);
-        break;
-      case JmolConstants.CALLBACK_MEASURE:
-      case JmolConstants.CALLBACK_CLICK:
-      default:
-        System.err.println("Unhandled callback " + type + " " + data);
-        break;
-      }
-    } catch (Exception e)
+    if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
     {
-      Cache.log.warn("Squashed Jmol callback handler error: ", e);
+      repaint();
+      return;
     }
-  }
+    setChainMenuItems(jmb.chainNames);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
 
-  @Override
-  public boolean notifyEnabled(int callbackPick)
-  {
-    switch (callbackPick)
-    {
-    case JmolConstants.CALLBACK_ECHO:
-    case JmolConstants.CALLBACK_LOADSTRUCT:
-    case JmolConstants.CALLBACK_MEASURE:
-    case JmolConstants.CALLBACK_MESSAGE:
-    case JmolConstants.CALLBACK_PICK:
-    case JmolConstants.CALLBACK_SCRIPT:
-    case JmolConstants.CALLBACK_HOVER:
-    case JmolConstants.CALLBACK_ERROR:
-      return true;
-    case JmolConstants.CALLBACK_CLICK:
-    case JmolConstants.CALLBACK_ANIMFRAME:
-    case JmolConstants.CALLBACK_MINIMIZATION:
-    case JmolConstants.CALLBACK_RESIZE:
-    case JmolConstants.CALLBACK_SYNC:
-    }
-    return false;
+    this.setTitle(jmb.getViewerTitle());
   }
 
-  @Override
-  public void setCallbackFunction(String callbackType,
-          String callbackFunction)
+  public void setJalviewColourScheme(ColourSchemeI ucs)
   {
-    Cache.log.debug("Ignoring set-callback request to associate "
-            + callbackType + " with function " + callbackFunction);
-
+    jmb.setJalviewColourScheme(ucs);
+    
   }
 
 }
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
new file mode 100644
index 0000000..831fd5a
--- /dev/null
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -0,0 +1,130 @@
+/**
+ * 
+ */
+package jalview.gui;
+
+import java.util.Vector;
+
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+
+import org.jmol.popup.JmolPopup;
+
+class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+{
+
+  /**
+   * 
+   */
+  private AppJmol appJmolWindow;
+
+  public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
+          SequenceI[] seq, String[] chains, String protocol)
+  {
+    super(pdbentry, seq, chains, protocol);
+    appJmolWindow = appJmol;
+  }
+  FeatureRenderer fr=null;
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer()
+  {
+    if (appJmolWindow.ap.av.showSequenceFeatures)
+    {
+      if (fr == null)
+      {
+        fr = new FeatureRenderer(appJmolWindow.ap);
+      }
+
+      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
+                      .getFeatureRenderer());
+    }
+
+    return fr;
+  }
+
+  @Override
+  public jalview.api.SequenceRenderer getSequenceRenderer()
+  {
+    return new SequenceRenderer(appJmolWindow.ap.av);
+  }
+
+  public void sendConsoleEcho(String strEcho)
+  {
+    if (appJmolWindow.scriptWindow != null)
+    {
+      appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+    }
+  }
+
+  public void sendConsoleMessage(String strStatus)
+  {
+    if (appJmolWindow.scriptWindow!=null && strStatus != null
+            )
+      //      && !strStatus.equals("Script completed"))
+      // should we squash the script completed string ?
+    {
+      appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+    }
+  }
+
+  @Override
+  public void showUrl(String url, String target)
+  {
+    try {
+      jalview.util.BrowserLauncher.openURL(url);
+    } catch (Exception e) {
+      Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+      // TODO: 2.6 : warn user if browser was not configured.
+    }
+  }
+
+  @Override
+  public void updateUI()
+  {
+    // appJmolWindow.repaint();
+    appJmolWindow.updateTitleAndMenus();
+  }
+
+  public void updateColours(Object source)
+  {
+    AlignmentPanel ap = (AlignmentPanel) source;
+    if (appJmolWindow.ap.alignFrame.getCurrentView()!=ap.av)
+      return;
+    
+    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+  }
+
+  public void notifyScriptTermination(String strStatus, int msWalltime)
+  {
+    if (appJmolWindow.scriptWindow != null)
+      appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+  }
+
+  public void showUrl(String url)
+  {
+    showUrl(url,"jmol");
+  }
+
+  public void newJmolPopup(boolean translateLocale, String menuName,
+          boolean asPopup)
+  {
+
+    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+            asPopup);
+  }
+  public synchronized void addSequence(SequenceI[] seq)
+  {
+    Vector v = new Vector();
+    for (int i = 0; i < sequence.length; i++)
+      v.addElement(sequence[i]);
+
+    for (int i = 0; i < seq.length; i++)
+      if (!v.contains(seq[i]))
+        v.addElement(seq[i]);
+
+    SequenceI[] tmp = new SequenceI[v.size()];
+    v.copyInto(tmp);
+    sequence = tmp;
+  }
+}
\ No newline at end of file
diff --git a/src/jalview/gui/ScriptWindow.java b/src/jalview/gui/ScriptWindow.java
index de31fcf..652830d 100644
--- a/src/jalview/gui/ScriptWindow.java
+++ b/src/jalview/gui/ScriptWindow.java
@@ -29,6 +29,7 @@ import org.jmol.i18n.GT;
 import org.jmol.util.Logger;
 import org.jmol.util.CommandHistory;
 
+// TODO: this class is copied in from jmol 11.0.2 - upgrade to 12.0.2 ?
 public final class ScriptWindow extends JPanel implements ActionListener,
         EnterListener
 {
@@ -53,7 +54,7 @@ public final class ScriptWindow extends JPanel implements ActionListener,
 
   public ScriptWindow(AppJmol appJmol)
   {
-    this.viewer = appJmol.viewer;
+    this.viewer = appJmol.jmb.viewer;
     this.appJmol = appJmol;
 
     setLayout(new BorderLayout());