patch for JAL-655

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index a314fd6..67b688c 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -317,6 +317,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
     String isel[] = new String[files.length];
     // reference structure - all others are superposed in it
     String[] targetC = new String[files.length];
+    String[] chainNames = new String[files.length];
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@ -379,6 +380,7 @@ public abstract class JalviewJmolBinding implements StructureListener,
             {
               targetC[pdbfnum] = ":" + mapping[m].getChain();
             }
+            chainNames[pdbfnum] = mapping[m].getPdbId()+targetC[pdbfnum];
             // move on to next pdb file
             s = sequence[pdbfnum].length;
             break;
@@ -461,7 +463,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
       {
         continue;
       }
-      command.append("compare ");
+      command.append("echo ");
+      command.append("\"Superposing (");
+      command.append(chainNames[pdbfnum]);
+      command.append(") against reference (");
+      command.append(chainNames[refStructure]);
+      command.append(")\";\ncompare ");
       command.append("{");
       command.append(1 + pdbfnum);
       command.append(".1} {");