JAL-3551

diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index 36957f5..652682a 100644 (file)
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -110,10 +110,11 @@ public class PymolCommands extends StructureCommandsBase
   {
     // https://pymolwiki.org/index.php/Super
     List<StructureCommandI> commands = new ArrayList<>();
-    String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
-    String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
-    commands.add(new StructureCommand("super", refAtomsAlphaOnly,
-            atomSpec2AlphaOnly));
+    String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, true)+" and (altloc '' or altloc 'a'))";
+    String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, true)+" and (altloc '' or altloc 'a'))";
+    // pair_fit mobile -> reference
+    commands.add(new StructureCommand("pair_fit", 
+            atomSpec2AlphaOnly, refAtomsAlphaOnly));
 
     /*
      * and show superposed residues as cartoon