From 8b5473a7ae1f9175c6ff66a013fa342636bdfd11 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 4 Feb 2021 17:50:29 +0000 Subject: [PATCH] JAL-2422 a fix and a fudge for two failing ChimeraX commands --- src/jalview/ext/rbvi/chimera/ChimeraXCommands.java | 3 +-- src/jalview/gui/JalviewChimeraXBindingModel.java | 5 +++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java index 314e6db..ad04fc9 100644 --- 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 startNotifications(String uri) { List 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 --- 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); -- 1.7.10.2