JAL-2422 a fix and a fudge for two failing ChimeraX commands

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index 314e6db..ad04fc9 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -28,7 +28,6 @@ import java.util.List;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
-import jalview.util.ColorUtils;
 
 /**
  * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
@@ -250,7 +249,7 @@ public class ChimeraXCommands extends ChimeraCommands
   public List<StructureCommandI> startNotifications(String uri)
   {
     List<StructureCommandI> cmds = new ArrayList<>();
-    cmds.add(new StructureCommand("info notify start models prefix ModelChanged jalview url " + uri));
+    cmds.add(new StructureCommand("info notify start models jalview prefix ModelChanged url " + uri));
     cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
     return cmds;
   }

diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
index 5b7a928..aecad00 100644 (file)
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -11,7 +11,6 @@ import jalview.ext.rbvi.chimera.ChimeraXCommands;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.structure.AtomSpec;
-import jalview.structure.StructureCommand;
 import jalview.structure.StructureSelectionManager;
 
 public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
@@ -42,7 +41,8 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
     int modelNumber = chimeraMaps.size() + 1;
     String command = "setattr #" + modelNumber + " models name "
             + pe.getId();
-    executeCommand(new StructureCommand(command), false);
+    // FIXME reinstate this for ChimeraX 1.2, see https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4211#comment:2
+ //   executeCommand(new StructureCommand(command), false);
     modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
             modelNumber, 0));
   }
@@ -93,6 +93,7 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
    * @param atomSpec
    * @return
    */
+  @Override
   protected AtomSpec parseAtomSpec(String atomSpec)
   {
     return AtomSpec.fromChimeraXAtomspec(atomSpec);