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

[jalview.git] / src / jalview / ext / rbvi / chimera / ChimeraXCommands.java

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);