JAL-3551 tidying, improved commands, fix Jmol model number derivation

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 844fb1b..4c19f6e 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -957,7 +957,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       if (modelFileNames[i].equalsIgnoreCase(pdbFile))
       {
-        return String.valueOf(i);
+        return String.valueOf(i + 1);
       }
     }
     return "";

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 7e04f39..c355abe 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -52,12 +52,13 @@ import java.util.Map;
  */
 public class ChimeraCommands extends StructureCommandsBase
 {
-  private static final StructureCommand SHOW_BACKBONE = new StructureCommand("~display all;chain @CA|P");
+  private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
+          "~display all;~ribbon;chain @CA|P");
 
   public static final String NAMESPACE_PREFIX = "jv_";
 
   private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
-          "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS");
+          "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
 
   private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
           "rainbow chain");
@@ -508,25 +509,27 @@ public class ChimeraCommands extends StructureCommandsBase
   }
 
   @Override
-  public List<StructureCommandI> superposeStructures(AtomSpecModel spec,
-          AtomSpecModel ref)
+  public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
+          AtomSpecModel spec)
   {
     /*
      * 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
+     * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
      */
     StringBuilder cmd = new StringBuilder();
-    String atomSpec = getAtomSpec(spec, true);
-    String refSpec = getAtomSpec(ref, true);
-    cmd.append("match ").append(atomSpec).append(" ").append(refSpec);
+    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");
 
@@ -621,7 +624,8 @@ public class ChimeraCommands extends StructureCommandsBase
        * restrict to alpha carbon, no alternative locations
        * (needed to ensuring matching atom counts for superposition)
        */
-      sb.append("@CA|P").append(NO_ALTLOCS);
+      // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
+      sb.append("@CA").append(NO_ALTLOCS);
     }
   }
 

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index 9636a6a..3341199 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -35,7 +35,7 @@ import java.util.List;
 public class ChimeraXCommands extends ChimeraCommands
 {
   private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
-          "~display all;show @CA|P pbonds");
+          "~display all;~ribbon;show @CA|P atoms");
 
   private static final StructureCommand FOCUS_VIEW = new StructureCommand(
           "view");
@@ -150,7 +150,8 @@ public class ChimeraXCommands extends ChimeraCommands
       appendModel(sb, model, atomSpec);
       if (alphaOnly)
       {
-        sb.append("@CA|P");
+        // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
+        sb.append("@CA");
       }
       // todo: is there ChimeraX syntax to exclude altlocs?
     }
@@ -195,16 +196,15 @@ public class ChimeraXCommands extends ChimeraCommands
   }
 
   @Override
-  public List<StructureCommandI> superposeStructures(AtomSpecModel spec,
-          AtomSpecModel ref)
+  public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
+          AtomSpecModel spec)
   {
     /*
      * Form ChimeraX match command to match spec to ref
      * 
      * match #1/A:2-94 toAtoms #2/A:1-93
      * 
-     * @see
-     * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
+     * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
      */
     StringBuilder cmd = new StringBuilder();
     String atomSpec = getAtomSpec(spec, true);

diff --git a/src/jalview/gui/ChimeraXViewFrame.java b/src/jalview/gui/ChimeraXViewFrame.java
index b33ccd6..56b2fe1 100644 (file)
--- a/src/jalview/gui/ChimeraXViewFrame.java
+++ b/src/jalview/gui/ChimeraXViewFrame.java
@@ -47,4 +47,12 @@ public class ChimeraXViewFrame extends ChimeraViewFrame
             ap.getStructureSelectionManager(), pdbentrys, seqs, null);
   }
 
+  @Override
+  protected void initMenus()
+  {
+    super.initMenus();
+
+    viewerActionMenu.setText("ChimeraX");
+  }
+
 }

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index 09451be..8f7f2c1 100644 (file)
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -73,6 +73,8 @@ public class PymolViewer extends StructureViewerBase
     binding.setColourBySequence(true);
     setSize(myWidth, myHeight);
     initMenus();
+    viewerActionMenu.setText("PyMOL");
+    updateTitleAndMenus();
 
     addingStructures = false;
     worker = new Thread(this);

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 0934488..8725b3d 100644 (file)
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -97,9 +97,9 @@ public interface StructureCommandsI
 
   /**
    * Returns a command to superpose structures by closest positioning of
-   * residues in {@code atomSpec} to the corresponding residues in {@ refAtoms}.
-   * If wanted, this may include commands to visually highlight the residues
-   * that were used for the superposition.
+   * residues in {@code atomSpec} to the corresponding residues in
+   * {@code refAtoms}. If wanted, this may include commands to visually
+   * highlight the residues that were used for the superposition.
    * 
    * @param refAtoms
    * @param atomSpec

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 8d8957c..db523f9 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -913,8 +913,7 @@ public abstract class AAStructureBindingModel
         {
           AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
           List<StructureCommandI> commands = commandGenerator
-                  .superposeStructures(refAtoms,
-                  atomSpec);
+                  .superposeStructures(refAtoms, atomSpec);
           List<String> replies = executeCommands(commands, true, null);
           for (String reply : replies)
           {