X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=bfad8fb7e1dee597505a432f184cceff622d6646;hb=0b6e9403e96ee9f0d41211b2f90130ff850c4e98;hp=61adefefbc38ade716820d283bdacd4267f28e48;hpb=6cb920bb7a7f285a165cd34b3429dabba71f7518;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 61adefe..bfad8fb 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,30 +20,19 @@ */ package jalview.ext.rbvi.chimera; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.MappedFeatures; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.gui.Desktop; -import jalview.renderer.seqfeatures.FeatureColourFinder; -import jalview.structure.StructureCommandsBase; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.ColorUtils; -import jalview.util.Comparison; +import java.util.Locale; import java.awt.Color; import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedHashMap; +import java.util.Arrays; import java.util.List; import java.util.Map; -import java.util.Map.Entry; + +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsBase; +import jalview.util.ColorUtils; /** * Routines for generating Chimera commands for Jalview/Chimera binding @@ -53,531 +42,53 @@ import java.util.Map.Entry; */ public class ChimeraCommands extends StructureCommandsBase { - public static final String NAMESPACE_PREFIX = "jv_"; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html + private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus"); - protected static final String CMD_SEPARATOR = ";"; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr + private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr"); - private static final String CMD_COLOUR_BY_CHARGE = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS"; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html + private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really"); - private static final String CMD_COLOUR_BY_CHAIN = "rainbow chain"; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html + private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection"); - @Override - public String[] colourBySequence( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, - AlignmentViewPanel viewPanel) - { - Map colourMap = buildColoursMap(ssm, files, - sequence, sr, viewPanel); + private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models"); - List colourCommands = buildColourCommands(colourMap); - - return colourCommands.toArray(new String[colourCommands.size()]); - } - - /** - * Traverse the map of colours/models/chains/positions to construct a list of - * 'color' commands (one per distinct colour used). The format of each command - * is - * - * 
-   * 
 
-   * color colorname #modelnumber:range.chain 
-   * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
-   * 

-   *
- * - * @param colourMap - * @return - */ - protected List buildColourCommands( - Map colourMap) - { - /* - * This version concatenates all commands into a single String (semi-colon - * delimited). If length limit issues arise, refactor to return one color - * command per colour. - */ - List commands = new ArrayList<>(); - StringBuilder sb = new StringBuilder(256); - boolean firstColour = true; - for (Object key : colourMap.keySet()) - { - Color colour = (Color) key; - String colourCode = ColorUtils.toTkCode(colour); - if (!firstColour) - { - sb.append("; "); - } - firstColour = false; - final AtomSpecModel colourData = colourMap.get(colour); - sb.append(getColourCommand(colourData, colourCode)); - } - commands.add(sb.toString()); - return commands; - } + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection + private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue"); - protected String getColourCommand(AtomSpecModel colourData, - String colourCode) - { - return "color " + colourCode + " " + colourData.getAtomSpec(); - } + private static final StructureCommand SHOW_BACKBONE = new StructureCommand( + "~display all;~ribbon;chain @CA|P"); - /** - * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and - * builds a Chimera format atom spec - * - * @param modelAndChainRanges - */ - protected static String getAtomSpec( - Map>> modelAndChainRanges) - { - StringBuilder sb = new StringBuilder(128); - boolean firstModelForColour = true; - for (Integer model : modelAndChainRanges.keySet()) - { - boolean firstPositionForModel = true; - if (!firstModelForColour) - { - sb.append("|"); - } - firstModelForColour = false; - sb.append("#").append(model).append(":"); - - final Map> modelData = modelAndChainRanges - .get(model); - for (String chain : modelData.keySet()) - { - boolean hasChain = !"".equals(chain.trim()); - for (int[] range : modelData.get(chain)) - { - if (!firstPositionForModel) - { - sb.append(","); - } - if (range[0] == range[1]) - { - sb.append(range[0]); - } - else - { - sb.append(range[0]).append("-").append(range[1]); - } - if (hasChain) - { - sb.append(".").append(chain); - } - firstPositionForModel = false; - } - } - } - return sb.toString(); - } - - /** - * 
-   * Build a data structure which records contiguous subsequences for each colour. 
-   * From this we can easily generate the Chimera command for colour by sequence.
-   * Color
-   *     Model number
-   *         Chain
-   *             list of start/end ranges
-   * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
-   *
- * - * @param ssm - * @param files - * @param sequence - * @param sr - * @param viewPanel - * @return - */ - protected static Map buildColoursMap( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, - AlignmentViewPanel viewPanel) - { - FeatureRenderer fr = viewPanel.getFeatureRenderer(); - FeatureColourFinder finder = new FeatureColourFinder(fr); - AlignViewportI viewport = viewPanel.getAlignViewport(); - HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); - AlignmentI al = viewport.getAlignment(); - Map colourMap = new LinkedHashMap<>(); - Color lastColour = null; - - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - final int modelNumber = pdbfnum + getModelStartNo(); - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - { - continue; - } - - int startPos = -1, lastPos = -1; - String lastChain = ""; - for (int s = 0; s < sequence[pdbfnum].length; s++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - final SequenceI seq = sequence[pdbfnum][s]; - if (mapping[m].getSequence() == seq - && (sp = al.findIndex(seq)) > -1) - { - SequenceI asp = al.getSequenceAt(sp); - for (int r = 0; r < asp.getLength(); r++) - { - // no mapping to gaps in sequence - if (Comparison.isGap(asp.getCharAt(r))) - { - continue; - } - int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - - if (pos < 1 || pos == lastPos) - { - continue; - } - - Color colour = sr.getResidueColour(seq, r, finder); - - /* - * darker colour for hidden regions - */ - if (!cs.isVisible(r)) - { - colour = Color.GRAY; - } - - final String chain = mapping[m].getChain(); - - /* - * Just keep incrementing the end position for this colour range - * _unless_ colour, PDB model or chain has changed, or there is a - * gap in the mapped residue sequence - */ - final boolean newColour = !colour.equals(lastColour); - final boolean nonContig = lastPos + 1 != pos; - final boolean newChain = !chain.equals(lastChain); - if (newColour || nonContig || newChain) - { - if (startPos != -1) - { - addAtomSpecRange(colourMap, lastColour, modelNumber, - startPos, lastPos, lastChain); - } - startPos = pos; - } - lastColour = colour; - lastPos = pos; - lastChain = chain; - } - // final colour range - if (lastColour != null) - { - addAtomSpecRange(colourMap, lastColour, modelNumber, startPos, - lastPos, lastChain); - } - // break; - } - } - } - } - return colourMap; - } - - /** - * Returns the lowest model number used by the structure viewer - * - * @return - */ - protected static int getModelStartNo() - { - return 0; - } + private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( + "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); - /** - * Helper method to add one contiguous range to the AtomSpec model for the given - * value (creating the model if necessary). As used by Jalview, {@code value} is - *
    - *
  • a colour, when building a 'colour structure by sequence' command
    • - *
  • a feature value, when building a 'set Chimera attributes from features' - * command
    • - *
- * - * @param map - * @param value - * @param model - * @param startPos - * @param endPos - * @param chain - */ - protected static final void addAtomSpecRange( - Map map, - Object value, int model, int startPos, int endPos, String chain) - { - /* - * Get/initialize map of data for the colour - */ - AtomSpecModel atomSpec = map.get(value); - if (atomSpec == null) - { - atomSpec = new AtomSpecModel(); - map.put(value, atomSpec); - } + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html + private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand( + "rainbow chain"); - atomSpec.addRange(model, startPos, endPos, chain); - } + // Chimera clause to exclude alternate locations in atom selection + private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; - /** - * Constructs and returns Chimera commands to set attributes on residues - * corresponding to features in Jalview. Attribute names are the Jalview feature - * type, with a "jv_" prefix. - * - * @param ssm - * @param files - * @param seqs - * @param viewPanel - * @return - */ @Override - public String[] setAttributesForFeatures( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) + public StructureCommandI colourResidues(String atomSpec, Color colour) { - Map> featureMap = buildFeaturesMap( - ssm, files, seqs, viewPanel); - - List commands = buildSetAttributeCommands(featureMap); - - return commands.toArray(new String[commands.size()]); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html + String colourCode = getColourString(colour); + return new StructureCommand("color " + colourCode + " " + atomSpec); } /** - * 
-   * Helper method to build a map of 
-   *   { featureType, { feature value, AtomSpecModel } }
-   *
+ * Returns a colour formatted suitable for use in viewer command syntax * - * @param ssm - * @param files - * @param seqs - * @param viewPanel + * @param colour * @return */ - protected static Map> buildFeaturesMap( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) + protected String getColourString(Color colour) { - Map> theMap = new LinkedHashMap<>(); - - FeatureRenderer fr = viewPanel.getFeatureRenderer(); - if (fr == null) - { - return theMap; - } - - AlignViewportI viewport = viewPanel.getAlignViewport(); - List visibleFeatures = fr.getDisplayedFeatureTypes(); - - /* - * if alignment is showing features from complement, we also transfer - * these features to the corresponding mapped structure residues - */ - boolean showLinkedFeatures = viewport.isShowComplementFeatures(); - List complementFeatures = new ArrayList<>(); - FeatureRenderer complementRenderer = null; - if (showLinkedFeatures) - { - AlignViewportI comp = fr.getViewport().getCodingComplement(); - if (comp != null) - { - complementRenderer = Desktop.getAlignFrameFor(comp) - .getFeatureRenderer(); - complementFeatures = complementRenderer.getDisplayedFeatureTypes(); - } - } - if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) - { - return theMap; - } - - AlignmentI alignment = viewPanel.getAlignment(); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - final int modelNumber = pdbfnum + getModelStartNo(); - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - { - continue; - } - - for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) - { - for (int m = 0; m < mapping.length; m++) - { - final SequenceI seq = seqs[pdbfnum][seqNo]; - int sp = alignment.findIndex(seq); - StructureMapping structureMapping = mapping[m]; - if (structureMapping.getSequence() == seq && sp > -1) - { - /* - * found a sequence with a mapping to a structure; - * now scan its features - */ - if (!visibleFeatures.isEmpty()) - { - scanSequenceFeatures(visibleFeatures, structureMapping, seq, - theMap, modelNumber); - } - if (showLinkedFeatures) - { - scanComplementFeatures(complementRenderer, structureMapping, - seq, theMap, modelNumber); - } - } - } - } - } - return theMap; - } - - /** - * Scans visible features in mapped positions of the CDS/peptide complement, and - * adds any found to the map of attribute values/structure positions - * - * @param complementRenderer - * @param structureMapping - * @param seq - * @param theMap - * @param modelNumber - */ - protected static void scanComplementFeatures( - FeatureRenderer complementRenderer, - StructureMapping structureMapping, SequenceI seq, - Map> theMap, int modelNumber) - { - /* - * for each sequence residue mapped to a structure position... - */ - for (int seqPos : structureMapping.getMapping().keySet()) - { - /* - * find visible complementary features at mapped position(s) - */ - MappedFeatures mf = complementRenderer - .findComplementFeaturesAtResidue(seq, seqPos); - if (mf != null) - { - for (SequenceFeature sf : mf.features) - { - String type = sf.getType(); - - /* - * Don't copy features which originated from Chimera - */ - if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP - .equals(sf.getFeatureGroup())) - { - continue; - } - - /* - * record feature 'value' (score/description/type) as at the - * corresponding structure position - */ - List mappedRanges = structureMapping - .getPDBResNumRanges(seqPos, seqPos); - - if (!mappedRanges.isEmpty()) - { - String value = sf.getDescription(); - if (value == null || value.length() == 0) - { - value = type; - } - float score = sf.getScore(); - if (score != 0f && !Float.isNaN(score)) - { - value = Float.toString(score); - } - Map featureValues = theMap.get(type); - if (featureValues == null) - { - featureValues = new HashMap<>(); - theMap.put(type, featureValues); - } - for (int[] range : mappedRanges) - { - addAtomSpecRange(featureValues, value, modelNumber, range[0], - range[1], structureMapping.getChain()); - } - } - } - } - } - } - - /** - * Inspect features on the sequence; for each feature that is visible, determine - * its mapped ranges in the structure (if any) according to the given mapping, - * and add them to the map. - * - * @param visibleFeatures - * @param mapping - * @param seq - * @param theMap - * @param modelNumber - */ - protected static void scanSequenceFeatures(List visibleFeatures, - StructureMapping mapping, SequenceI seq, - Map> theMap, int modelNumber) - { - List sfs = seq.getFeatures().getPositionalFeatures( - visibleFeatures.toArray(new String[visibleFeatures.size()])); - for (SequenceFeature sf : sfs) - { - String type = sf.getType(); - - /* - * Don't copy features which originated from Chimera - */ - if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP - .equals(sf.getFeatureGroup())) - { - continue; - } - - List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), - sf.getEnd()); - - if (!mappedRanges.isEmpty()) - { - String value = sf.getDescription(); - if (value == null || value.length() == 0) - { - value = type; - } - float score = sf.getScore(); - if (score != 0f && !Float.isNaN(score)) - { - value = Float.toString(score); - } - Map featureValues = theMap.get(type); - if (featureValues == null) - { - featureValues = new HashMap<>(); - theMap.put(type, featureValues); - } - for (int[] range : mappedRanges) - { - addAtomSpecRange(featureValues, value, modelNumber, range[0], - range[1], mapping.getChain()); - } - } - } + return ColorUtils.toTkCode(colour); } /** @@ -595,10 +106,11 @@ public class ChimeraCommands extends StructureCommandsBase * @param featureMap * @return */ - protected List buildSetAttributeCommands( + @Override + public List setAttributes( Map> featureMap) { - List commands = new ArrayList<>(); + List commands = new ArrayList<>(); for (String featureType : featureMap.keySet()) { String attributeName = makeAttributeName(featureType); @@ -620,7 +132,7 @@ public class ChimeraCommands extends StructureCommandsBase AtomSpecModel atomSpecModel = values.get(value); String featureValue = value.toString(); featureValue = featureValue.replaceAll("\\'", "'"); - String cmd = getSetAttributeCommand(attributeName, featureValue, + StructureCommandI cmd = setAttribute(attributeName, featureValue, atomSpecModel); commands.add(cmd); } @@ -642,15 +154,15 @@ public class ChimeraCommands extends StructureCommandsBase * @param atomSpecModel * @return */ - protected String getSetAttributeCommand(String attributeName, + protected StructureCommandI setAttribute(String attributeName, String attributeValue, AtomSpecModel atomSpecModel) { StringBuilder sb = new StringBuilder(128); sb.append("setattr res ").append(attributeName).append(" '") .append(attributeValue).append("' "); - sb.append(atomSpecModel.getAtomSpec()); - return sb.toString(); + sb.append(getAtomSpec(atomSpecModel, false)); + return new StructureCommand(sb.toString()); } /** @@ -662,23 +174,16 @@ public class ChimeraCommands extends StructureCommandsBase * @return * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html */ - protected static String makeAttributeName(String featureType) + @Override + protected String makeAttributeName(String featureType) { - StringBuilder sb = new StringBuilder(); - if (featureType != null) - { - for (char c : featureType.toCharArray()) - { - sb.append(Character.isLetterOrDigit(c) ? c : '_'); - } - } - String attName = NAMESPACE_PREFIX + sb.toString(); + String attName = super.makeAttributeName(featureType); /* * Chimera treats an attribute name ending in 'color' as colour-valued; * Jalview doesn't, so prevent this by appending an underscore */ - if (attName.toUpperCase().endsWith("COLOR")) + if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR")) { attName += "_"; } @@ -687,50 +192,38 @@ public class ChimeraCommands extends StructureCommandsBase } @Override - public String colourByChain() + public StructureCommandI colourByChain() { - return CMD_COLOUR_BY_CHAIN; + return COLOUR_BY_CHAIN; } @Override - public String colourByCharge() + public List colourByCharge() { - return CMD_COLOUR_BY_CHARGE; + return Arrays.asList(COLOUR_BY_CHARGE); } @Override - public String colourByResidues(Map colours) + public String getResidueSpec(String residue) { - StringBuilder cmd = new StringBuilder(12 * colours.size()); - - /* - * concatenate commands like - * color #4949b6 ::VAL - */ - for (Entry entry : colours.entrySet()) - { - String colorSpec = ColorUtils.toTkCode(entry.getValue()); - String resCode = entry.getKey(); - cmd.append("color ").append(colorSpec).append(" ::").append(resCode) - .append(CMD_SEPARATOR); - } - return cmd.toString(); + return "::" + residue; } @Override - public String setBackgroundColour(Color col) + public StructureCommandI setBackgroundColour(Color col) { - return "set bgColor " + ColorUtils.toTkCode(col); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor + return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col)); } @Override - public String focusView() + public StructureCommandI focusView() { - return "focus"; + return FOCUS_VIEW; } @Override - public String showChains(List toShow) + public List showChains(List toShow) { /* * Construct a chimera command like @@ -761,7 +254,195 @@ public class ChimeraCommands extends StructureCommandsBase */ final String command = "~display #*; ~ribbon #*; ribbon :" + cmd.toString(); - return command; + return Arrays.asList(new StructureCommand(command)); + } + + @Override + public List superposeStructures(AtomSpecModel ref, + AtomSpecModel spec, boolean isNucleotide) + { + /* + * Form Chimera match command to match spec to ref + * (the first set of atoms are moved on to the second) + * + * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA + * + * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html + */ + StringBuilder cmd = new StringBuilder(); + String atomSpecAlphaOnly = getAtomSpec(spec, true); + String refSpecAlphaOnly = getAtomSpec(ref, true); + cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly); + + /* + * show superposed residues as ribbon + */ + String atomSpec = getAtomSpec(spec, false); + String refSpec = getAtomSpec(ref, false); + cmd.append("; ribbon "); + cmd.append(atomSpec).append("|").append(refSpec).append("; focus"); + + return Arrays.asList(new StructureCommand(cmd.toString())); + } + + @Override + public StructureCommandI openCommandFile(String path) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html + return new StructureCommand("open cmd:" + path); + } + + @Override + public StructureCommandI saveSession(String filepath) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html + return new StructureCommand("save " + filepath); + } + + /** + * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera + * atomspec string, e.g. + * + * 
+   * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
+   *
+ * + * where + *
    + *
  • #0 is a model number
    • + *
  • 15 or 70-72 is a residue number, or range of residue numbers
    • + *
  • .A is a chain identifier
    • + *
  • residue ranges are separated by comma
    • + *
  • atomspecs for distinct models are separated by | (or)
    • + *
+ * + * 
+   * 
+   * @param model
+   * @param alphaOnly
+   * @return
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+   */
+  @Override
+  public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+  {
+    StringBuilder sb = new StringBuilder(128);
+    boolean firstModel = true;
+    for (String model : atomSpec.getModels())
+    {
+      if (!firstModel)
+      {
+        sb.append("|");
+      }
+      firstModel = false;
+      appendModel(sb, model, atomSpec, alphaOnly);
+    }
+    return sb.toString();
+  }
+
+  /**
+   * A helper method to append an atomSpec string for atoms in the given model
+   * 
+   * @param sb
+   * @param model
+   * @param atomSpec
+   * @param alphaOnly
+   */
+  protected void appendModel(StringBuilder sb, String model,
+          AtomSpecModel atomSpec, boolean alphaOnly)
+  {
+    sb.append("#").append(model).append(":");
+
+    boolean firstPositionForModel = true;
+
+    for (String chain : atomSpec.getChains(model))
+    {
+      chain = " ".equals(chain) ? chain : chain.trim();
+
+      List rangeList = atomSpec.getRanges(model, chain);
+      for (int[] range : rangeList)
+      {
+        appendRange(sb, range[0], range[1], chain, firstPositionForModel,
+                false);
+        firstPositionForModel = false;
+      }
+    }
+    if (alphaOnly)
+    {
+      /*
+       * restrict to alpha carbon, no alternative locations
+       * (needed to ensuring matching atom counts for superposition)
+       */
+      // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
+      sb.append("@CA").append(NO_ALTLOCS);
+    }
+  }
+
+  @Override
+  public List showBackbone()
+  {
+    return Arrays.asList(SHOW_BACKBONE);
+  }
+
+  @Override
+  public StructureCommandI loadFile(String file)
+  {
+    return new StructureCommand("open " + file);
+  }
+
+  @Override
+  public StructureCommandI openSession(String filepath)
+  {
+    // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+    // this version of the command has no dependency on file extension
+    return new StructureCommand("open chimera:" + filepath);
+  }
+
+  @Override
+  public StructureCommandI closeViewer()
+  {
+    return CLOSE_CHIMERA;
+  }
+
+  @Override
+  public List startNotifications(String uri)
+  {
+    // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
+    List cmds = new ArrayList<>();
+    cmds.add(new StructureCommand("listen start models url " + uri));
+    cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+    return cmds;
+  }
+
+  @Override
+  public List stopNotifications()
+  {
+    List cmds = new ArrayList<>();
+    cmds.add(STOP_NOTIFY_MODELS);
+    cmds.add(STOP_NOTIFY_SELECTION);
+    return cmds;
+  }
+
+  @Override
+  public StructureCommandI getSelectedResidues()
+  {
+    return GET_SELECTION;
+  }
+
+  @Override
+  public StructureCommandI listResidueAttributes()
+  {
+    return LIST_RESIDUE_ATTRIBUTES;
+  }
+
+  @Override
+  public StructureCommandI getResidueAttributes(String attName)
+  {
+    // this alternative command
+    // list residues spec ':*/attName' attr attName
+    // doesn't report 'None' values (which is good), but
+    // fails for 'average.bfactor' (which is bad):
+    return new StructureCommand("list residues attr '" + attName + "'");
   }
 
 }