X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=8b67ad9d023ec23c3c1cd6cc6f1b7f2ad53f798f;hb=3efc24bc7b7855ff135fa96e35ab1004eaeb4f5e;hp=25f6aecbb795b1d0361489612ec35847f9122515;hpb=dae56c38c3f14e96308540c30f35ca8f1d917edf;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 25f6aec..8b67ad9 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -40,6 +40,7 @@ import jalview.structure.StructureCommandI;
 import jalview.structure.StructureCommandsBase;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.StructureCommandsI.AtomSpecType;
 import jalview.util.Comparison;
 import jalview.util.Platform;
 
@@ -178,7 +179,7 @@ public class JmolCommands extends StructureCommandsBase
    */
   @Override
   public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
-          AtomSpecModel atomSpec)
+          AtomSpecModel atomSpec, AtomSpecType backbone)
   {
     StringBuilder sb = new StringBuilder(64);
     String refModel = refAtoms.getModels().iterator().next();
@@ -190,16 +191,16 @@ public class JmolCommands extends StructureCommandsBase
      * command examples don't include modelspec with atoms, getAtomSpec does;
      * it works, so leave it as it is for simplicity
      */
-    sb.append(getAtomSpec(atomSpec, true)).append("}{");
-    sb.append(getAtomSpec(refAtoms, true)).append("}");
+    sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
+    sb.append(getAtomSpec(refAtoms, backbone)).append("}");
     sb.append(" ROTATE TRANSLATE ");
     sb.append(getCommandSeparator());
 
     /*
      * show residues used for superposition as ribbon
      */
-    sb.append("select ").append(getAtomSpec(atomSpec, false)).append("|");
-    sb.append(getAtomSpec(refAtoms, false)).append(getCommandSeparator())
+    sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
+    sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
             .append("cartoons");
 
     return Arrays.asList(new StructureCommand(sb.toString()));
@@ -250,7 +251,7 @@ public class JmolCommands extends StructureCommandsBase
    * a separate clause in the {@code compare} (superposition) command.
    */
   @Override
-  public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+  public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
   {
     StringBuilder sb = new StringBuilder(128);