2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.rbvi.chimera;
23 import java.awt.Color;
24 import java.net.BindException;
25 import java.util.ArrayList;
26 import java.util.LinkedHashMap;
27 import java.util.List;
30 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
31 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
32 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
33 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
35 import jalview.api.AlignmentViewPanel;
36 import jalview.api.FeatureRenderer;
37 import jalview.api.SequenceRenderer;
38 import jalview.bin.Cache;
39 import jalview.datamodel.AlignmentI;
40 import jalview.datamodel.ColumnSelection;
41 import jalview.datamodel.PDBEntry;
42 import jalview.datamodel.SequenceI;
43 import jalview.httpserver.AbstractRequestHandler;
44 import jalview.schemes.ColourSchemeI;
45 import jalview.schemes.ResidueProperties;
46 import jalview.structure.AtomSpec;
47 import jalview.structure.StructureMappingcommandSet;
48 import jalview.structure.StructureSelectionManager;
49 import jalview.structures.models.AAStructureBindingModel;
50 import jalview.util.MessageManager;
52 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
54 // Chimera clause to exclude alternate locations in atom selection
55 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
57 private static final String COLOURING_CHIMERA = MessageManager
58 .getString("status.colouring_chimera");
60 private static final boolean debug = false;
62 private static final String PHOSPHORUS = "P";
64 private static final String ALPHACARBON = "CA";
67 * Object through which we talk to Chimera
69 private ChimeraManager viewer;
72 * Object which listens to Chimera notifications
74 private AbstractRequestHandler chimeraListener;
77 * set if chimera state is being restored from some source - instructs binding
78 * not to apply default display style when structure set is updated for first
81 private boolean loadingFromArchive = false;
84 * flag to indicate if the Chimera viewer should ignore sequence colouring
85 * events from the structure manager because the GUI is still setting up
87 private boolean loadingFinished = true;
90 * state flag used to check if the Chimera viewer's paint method can be called
92 private boolean finishedInit = false;
94 public String fileLoadingError;
97 * Map of ChimeraModel objects keyed by PDB full local file name
99 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
102 * the default or current model displayed if the model cannot be identified
103 * from the selection message
105 private int frameNo = 0;
107 private String lastCommand;
109 private boolean loadedInline;
112 * current set of model filenames loaded
114 String[] modelFileNames = null;
116 String lastMousedOverAtomSpec;
118 private List<String> lastReply;
121 * incremented every time a load notification is successfully handled -
122 * lightweight mechanism for other threads to detect when they can start
123 * referring to new structures.
125 private long loadNotifiesHandled = 0;
128 * Open a PDB structure file in Chimera and set up mappings from Jalview.
130 * We check if the PDB model id is already loaded in Chimera, if so don't
131 * reopen it. This is the case if Chimera has opened a saved session file.
136 public boolean openFile(PDBEntry pe)
138 String file = pe.getFile();
141 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
142 List<ChimeraModel> oldList = viewer.getModelList();
143 boolean alreadyOpen = false;
146 * If Chimera already has this model, don't reopen it, but do remap it.
148 for (ChimeraModel open : oldList)
150 if (open.getModelName().equals(pe.getId()))
153 modelsToMap.add(open);
158 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
159 * the model name(s) added by Chimera.
163 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
164 List<ChimeraModel> newList = viewer.getModelList();
165 // JAL-1728 newList.removeAll(oldList) does not work
166 for (ChimeraModel cm : newList)
168 if (cm.getModelName().equals(pe.getId()))
175 chimeraMaps.put(file, modelsToMap);
177 if (getSsm() != null)
179 getSsm().addStructureViewerListener(this);
180 // ssm.addSelectionListener(this);
181 FeatureRenderer fr = getFeatureRenderer(null);
189 } catch (Exception q)
191 log("Exception when trying to open model " + file + "\n"
207 public JalviewChimeraBinding(StructureSelectionManager ssm,
208 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
211 super(ssm, pdbentry, sequenceIs, chains, protocol);
212 viewer = new ChimeraManager(
213 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
217 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
218 * it to start listening
220 public void startChimeraListener()
224 chimeraListener = new ChimeraListener(this);
225 viewer.startListening(chimeraListener.getUri());
226 } catch (BindException e)
228 System.err.println("Failed to start Chimera listener: "
234 * Construct a title string for the viewer window based on the data Jalview
240 public String getViewerTitle(boolean verbose)
242 return getViewerTitle("Chimera", verbose);
246 * Tells Chimera to display only the specified chains
250 public void showChains(List<String> toshow)
253 * Construct a chimera command like
255 * ~display #*;~ribbon #*;ribbon :.A,:.B
257 StringBuilder cmd = new StringBuilder(64);
258 boolean first = true;
259 for (String chain : toshow)
265 cmd.append(":.").append(chain);
270 * could append ";focus" to this command to resize the display to fill the
271 * window, but it looks more helpful not to (easier to relate chains to the
274 final String command = "~display #*; ~ribbon #*; ribbon "
276 sendChimeraCommand(command, false);
280 * Close down the Jalview viewer and listener, and (optionally) the associated
283 public void closeViewer(boolean closeChimera)
285 getSsm().removeStructureViewerListener(this, this.getPdbFile());
288 viewer.exitChimera();
290 if (this.chimeraListener != null)
292 chimeraListener.shutdown();
293 chimeraListener = null;
298 releaseUIResources();
301 public void colourByChain()
303 colourBySequence = false;
304 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
308 * Constructs and sends a Chimera command to colour by charge
310 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
311 * <li>Lysine and Arginine (positive charge) blue</li>
312 * <li>Cysteine - yellow</li>
313 * <li>all others - white</li>
316 public void colourByCharge()
318 colourBySequence = false;
319 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
320 sendAsynchronousCommand(command, COLOURING_CHIMERA);
324 * Construct and send a command to align structures against a reference
325 * structure, based on one or more sequence alignments
328 * an array of alignments to process
329 * @param _refStructure
330 * an array of corresponding reference structures (index into pdb
331 * file array); if a negative value is passed, the first PDB file
332 * mapped to an alignment sequence is used as the reference for
335 * an array of corresponding hidden columns for each alignment
337 public void superposeStructures(AlignmentI[] _alignment,
338 int[] _refStructure, ColumnSelection[] _hiddenCols)
340 StringBuilder allComs = new StringBuilder(128);
341 String[] files = getPdbFile();
343 if (!waitForFileLoad(files))
349 StringBuilder selectioncom = new StringBuilder(256);
350 for (int a = 0; a < _alignment.length; a++)
352 int refStructure = _refStructure[a];
353 AlignmentI alignment = _alignment[a];
354 ColumnSelection hiddenCols = _hiddenCols[a];
356 if (refStructure >= files.length)
358 System.err.println("Ignoring invalid reference structure value "
364 * 'matched' array will hold 'true' for visible alignment columns where
365 * all sequences have a residue with a mapping to the PDB structure
367 boolean matched[] = new boolean[alignment.getWidth()];
368 for (int m = 0; m < matched.length; m++)
370 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
373 SuperposeData[] structures = new SuperposeData[files.length];
374 for (int f = 0; f < files.length; f++)
376 structures[f] = new SuperposeData(alignment.getWidth());
380 * Calculate the superposable alignment columns ('matched'), and the
381 * corresponding structure residue positions (structures.pdbResNo)
383 int candidateRefStructure = findSuperposableResidues(alignment,
384 matched, structures);
385 if (refStructure < 0)
388 * If no reference structure was specified, pick the first one that has
389 * a mapping in the alignment
391 refStructure = candidateRefStructure;
395 for (boolean b : matched)
404 // TODO: bail out here because superposition illdefined?
408 * Generate select statements to select regions to superimpose structures
410 String[] selcom = new String[files.length];
411 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
413 String chainCd = "." + structures[pdbfnum].chain;
416 StringBuilder molsel = new StringBuilder();
417 for (int r = 0; r < matched.length; r++)
421 int pdbResNum = structures[pdbfnum].pdbResNo[r];
422 if (lpos != pdbResNum - 1)
425 * discontiguous - append last residue now
429 molsel.append(String.valueOf(lpos));
430 molsel.append(chainCd);
438 * extending a contiguous run
443 * start the range selection
445 molsel.append(String.valueOf(lpos));
455 * and terminate final selection
459 molsel.append(String.valueOf(lpos));
460 molsel.append(chainCd);
462 if (molsel.length() > 1)
464 selcom[pdbfnum] = molsel.toString();
465 selectioncom.append("#").append(String.valueOf(pdbfnum))
467 selectioncom.append(selcom[pdbfnum]);
468 selectioncom.append(" ");
469 if (pdbfnum < files.length - 1)
471 selectioncom.append("| ");
476 selcom[pdbfnum] = null;
480 StringBuilder command = new StringBuilder(256);
481 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
483 if (pdbfnum == refStructure || selcom[pdbfnum] == null
484 || selcom[refStructure] == null)
488 if (command.length() > 0)
494 * Form Chimera match command, from the 'new' structure to the
495 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
497 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
500 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
502 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
503 command.append(selcom[pdbfnum]);
504 command.append("@").append(
505 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
506 // JAL-1757 exclude alternate CA locations
507 command.append(NO_ALTLOCS);
508 command.append(" ").append(getModelSpec(refStructure)).append(":");
509 command.append(selcom[refStructure]);
510 command.append("@").append(
511 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
512 command.append(NO_ALTLOCS);
514 if (selectioncom.length() > 0)
518 System.out.println("Select regions:\n" + selectioncom.toString());
519 System.out.println("Superimpose command(s):\n"
520 + command.toString());
522 allComs.append("~display all; chain @CA|P; ribbon ")
523 .append(selectioncom.toString())
524 .append(";" + command.toString());
527 if (selectioncom.length() > 0)
529 // TODO: visually distinguish regions that were superposed
530 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
532 selectioncom.setLength(selectioncom.length() - 1);
536 System.out.println("Select regions:\n" + selectioncom.toString());
538 allComs.append("; ~display all; chain @CA|P; ribbon ")
539 .append(selectioncom.toString()).append("; focus");
540 sendChimeraCommand(allComs.toString(), false);
546 * Helper method to construct model spec in Chimera format:
548 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
549 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
551 * Note for now we only ever choose the first of multiple models. This
552 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
553 * future if there is a need to select specific sub-models.
558 protected String getModelSpec(int pdbfnum)
560 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
566 * For now, the test for having sub-models is whether multiple Chimera
567 * models are mapped for the PDB file; the models are returned as a response
568 * to the Chimera command 'list models type molecule', see
569 * ChimeraManager.getModelList().
571 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
572 boolean hasSubModels = maps != null && maps.size() > 1;
573 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
577 * Launch Chimera, unless an instance linked to this object is already
578 * running. Returns true if chimera is successfully launched, or already
579 * running, else false.
583 public boolean launchChimera()
585 if (!viewer.isChimeraLaunched())
587 return viewer.launchChimera(StructureManager.getChimeraPaths());
589 if (viewer.isChimeraLaunched())
593 log("Failed to launch Chimera!");
598 * Answers true if the Chimera process is still running, false if ended or not
603 public boolean isChimeraRunning()
605 return viewer.isChimeraLaunched();
609 * Send a command to Chimera, and optionally log any responses.
614 public void sendChimeraCommand(final String command, boolean logResponse)
616 viewerCommandHistory(false);
617 if (lastCommand == null || !lastCommand.equals(command))
619 // trim command or it may never find a match in the replyLog!!
620 lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
621 if (logResponse && debug)
623 log("Response from command ('" + command + "') was:\n" + lastReply);
626 viewerCommandHistory(true);
627 lastCommand = command;
631 * Send a Chimera command asynchronously in a new thread. If the progress
632 * message is not null, display this message while the command is executing.
637 protected abstract void sendAsynchronousCommand(String command,
641 * colour any structures associated with sequences in the given alignment
642 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
643 * if colourBySequence is enabled.
645 public void colourBySequence(boolean showFeatures,
646 jalview.api.AlignmentViewPanel alignmentv)
648 if (!colourBySequence || !loadingFinished)
652 if (getSsm() == null)
656 String[] files = getPdbFile();
658 SequenceRenderer sr = getSequenceRenderer(alignmentv);
660 FeatureRenderer fr = null;
663 fr = getFeatureRenderer(alignmentv);
665 AlignmentI alignment = alignmentv.getAlignment();
667 for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
668 files, sr, fr, alignment))
670 for (String command : cpdbbyseq.commands)
672 sendAsynchronousCommand(command, COLOURING_CHIMERA);
684 protected StructureMappingcommandSet[] getColourBySequenceCommands(
685 String[] files, SequenceRenderer sr, FeatureRenderer fr,
686 AlignmentI alignment)
688 return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
689 getSequence(), sr, fr, alignment);
695 protected void executeWhenReady(String command)
698 sendChimeraCommand(command, false);
702 private void waitForChimera()
704 while (viewer != null && viewer.isBusy())
709 } catch (InterruptedException q)
715 // End StructureListener
716 // //////////////////////////
718 public Color getColour(int atomIndex, int pdbResNum, String chain,
721 if (getModelNum(pdbfile) < 0)
725 log("get model / residue colour attribute unimplemented");
730 * returns the current featureRenderer that should be used to colour the
737 public abstract FeatureRenderer getFeatureRenderer(
738 AlignmentViewPanel alignment);
741 * instruct the Jalview binding to update the pdbentries vector if necessary
742 * prior to matching the viewer's contents to the list of structure files
743 * Jalview knows about.
745 public abstract void refreshPdbEntries();
747 private int getModelNum(String modelFileName)
749 String[] mfn = getPdbFile();
754 for (int i = 0; i < mfn.length; i++)
756 if (mfn[i].equalsIgnoreCase(modelFileName))
765 * map between index of model filename returned from getPdbFile and the first
766 * index of models from this file in the viewer. Note - this is not trimmed -
767 * use getPdbFile to get number of unique models.
769 private int _modelFileNameMap[];
771 // ////////////////////////////////
772 // /StructureListener
774 public synchronized String[] getPdbFile()
778 return new String[0];
780 // if (modelFileNames == null)
782 // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
783 // _modelFileNameMap = new int[chimodels.size()];
785 // for (ChimeraModel chimodel : chimodels)
787 // String mdlName = chimodel.getModelName();
789 // modelFileNames = new String[j];
790 // // System.arraycopy(mset, 0, modelFileNames, 0, j);
793 return chimeraMaps.keySet().toArray(
794 modelFileNames = new String[chimeraMaps.size()]);
798 * map from string to applet
800 public Map getRegistryInfo()
802 // TODO Auto-generated method stub
807 * returns the current sequenceRenderer that should be used to colour the
814 public abstract SequenceRenderer getSequenceRenderer(
815 AlignmentViewPanel alignment);
818 * Construct and send a command to highlight zero, one or more atoms.
821 * Done by generating a command like (to 'highlight' position 44)
826 public void highlightAtoms(List<AtomSpec> atoms)
832 StringBuilder atomSpecs = new StringBuilder();
833 boolean first = true;
834 for (AtomSpec atom : atoms)
836 int pdbResNum = atom.getPdbResNum();
837 String chain = atom.getChain();
838 String pdbfile = atom.getPdbFile();
839 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
840 if (cms != null && !cms.isEmpty())
843 * Formatting as #0:34.A,#1:33.A doesn't work as desired, so instead we
844 * concatenate multiple 'show' commands
846 atomSpecs.append(first ? "" : ";show ");
848 atomSpecs.append("#" + cms.get(0).getModelNumber());
849 atomSpecs.append(":" + pdbResNum);
850 if (!chain.equals(" "))
852 atomSpecs.append("." + chain);
856 String atomSpec = atomSpecs.toString();
859 * Avoid repeated commands for the same residue
861 if (atomSpec.equals(lastMousedOverAtomSpec))
866 StringBuilder command = new StringBuilder(32);
867 viewerCommandHistory(false);
868 if (atomSpec.length() > 0)
870 command.append("show ").append(atomSpec);
871 viewer.sendChimeraCommand(command.toString(), false);
873 viewerCommandHistory(true);
874 this.lastMousedOverAtomSpec = atomSpec;
878 * Query Chimera for its current selection, and highlight it on the alignment
880 public void highlightChimeraSelection()
883 * Ask Chimera for its current selection
885 List<String> selection = viewer.getSelectedResidueSpecs();
888 * Parse model number, residue and chain for each selected position,
889 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
891 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
892 for (String atomSpec : selection)
894 int colonPos = atomSpec.indexOf(":");
897 continue; // malformed
900 int hashPos = atomSpec.indexOf("#");
901 String modelSubmodel = atomSpec.substring(hashPos + 1, colonPos);
902 int dotPos = modelSubmodel.indexOf(".");
906 modelId = Integer.valueOf(dotPos == -1 ? modelSubmodel
907 : modelSubmodel.substring(0, dotPos));
908 } catch (NumberFormatException e)
910 // ignore, default to model 0
913 String residueChain = atomSpec.substring(colonPos + 1);
914 dotPos = residueChain.indexOf(".");
915 int pdbResNum = Integer.parseInt(dotPos == -1 ? residueChain
916 : residueChain.substring(0, dotPos));
918 String chainId = dotPos == -1 ? "" : residueChain
919 .substring(dotPos + 1);
922 * Work out the pdbfilename from the model number
924 String pdbfilename = modelFileNames[frameNo];
925 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
927 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
929 if (cm.getModelNumber() == modelId)
931 pdbfilename = pdbfile;
936 atomSpecs.add(new AtomSpec(pdbfilename, chainId, pdbResNum, 0));
940 * Broadcast the selection (which may be empty, if the user just cleared all
943 getSsm().mouseOverStructure(atomSpecs);
946 private void log(String message)
948 System.err.println("## Chimera log: " + message);
951 private void viewerCommandHistory(boolean enable)
953 // log("(Not yet implemented) History "
954 // + ((debug || enable) ? "on" : "off"));
957 public long getLoadNotifiesHandled()
959 return loadNotifiesHandled;
962 public void setJalviewColourScheme(ColourSchemeI cs)
964 colourBySequence = false;
971 // Chimera expects RBG values in the range 0-1
972 final double normalise = 255D;
973 viewerCommandHistory(false);
974 StringBuilder command = new StringBuilder(128);
976 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
978 for (String res : residueSet)
980 Color col = cs.findColour(res.charAt(0));
981 command.append("color " + col.getRed() / normalise + ","
982 + col.getGreen() / normalise + "," + col.getBlue()
983 / normalise + " ::" + res + ";");
986 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
987 viewerCommandHistory(true);
991 * called when the binding thinks the UI needs to be refreshed after a Chimera
992 * state change. this could be because structures were loaded, or because an
993 * error has occurred.
995 public abstract void refreshGUI();
997 public void setLoadingFromArchive(boolean loadingFromArchive)
999 this.loadingFromArchive = loadingFromArchive;
1004 * @return true if Chimeral is still restoring state or loading is still going
1005 * on (see setFinsihedLoadingFromArchive)
1007 public boolean isLoadingFromArchive()
1009 return loadingFromArchive && !loadingFinished;
1013 * modify flag which controls if sequence colouring events are honoured by the
1014 * binding. Should be true for normal operation
1016 * @param finishedLoading
1018 public void setFinishedLoadingFromArchive(boolean finishedLoading)
1020 loadingFinished = finishedLoading;
1024 * Send the Chimera 'background solid <color>" command.
1027 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
1031 public void setBackgroundColour(Color col)
1033 viewerCommandHistory(false);
1034 double normalise = 255D;
1035 final String command = "background solid " + col.getRed() / normalise
1036 + "," + col.getGreen() / normalise + "," + col.getBlue()
1038 viewer.sendChimeraCommand(command, false);
1039 viewerCommandHistory(true);
1043 * Ask Chimera to save its session to the given file. Returns true if
1044 * successful, else false.
1049 public boolean saveSession(String filepath)
1051 if (isChimeraRunning())
1053 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1055 if (reply.contains("Session written"))
1062 .error("Error saving Chimera session: " + reply.toString());
1069 * Ask Chimera to open a session file. Returns true if successful, else false.
1070 * The filename must have a .py extension for this command to work.
1075 public boolean openSession(String filepath)
1077 sendChimeraCommand("open " + filepath, true);
1078 // todo: test for failure - how?
1082 public boolean isFinishedInit()
1084 return finishedInit;
1087 public void setFinishedInit(boolean finishedInit)
1089 this.finishedInit = finishedInit;
1093 * Returns a list of chains mapped in this viewer. Note this list is not
1094 * currently scoped per structure.
1098 public List<String> getChainNames()
1100 List<String> names = new ArrayList<String>();
1101 String[][] allNames = getChains();
1102 if (allNames != null)
1104 for (String[] chainsForPdb : allNames)
1106 if (chainsForPdb != null)
1108 for (String chain : chainsForPdb)
1110 if (chain != null && !names.contains(chain))
1122 * Send a 'focus' command to Chimera to recentre the visible display
1124 public void focusView()
1126 sendChimeraCommand("focus", false);