From cac1ed6669adb3fc93af536cfe3c5a5301e7b2ad Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 18 Apr 2014 10:56:53 +0100
Subject: [PATCH] JAL-1476 -  don't send broken commands to Jmol when no
 columns exist to superimpose structures

---
 src/jalview/ext/jmol/JalviewJmolBinding.java |   43 ++++++++++++++++----------
 1 file changed, 26 insertions(+), 17 deletions(-)

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8dfb9fd..46c94c4 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -543,22 +543,27 @@ public abstract class JalviewJmolBinding implements StructureListener,
             molsel.append(chainCd);
             molsel.append("}");
           }
-          selcom[pdbfnum] = molsel.toString();
-          selectioncom.append("((");
-          selectioncom.append(selcom[pdbfnum].substring(1,
-                  selcom[pdbfnum].length() - 1));
-          selectioncom.append(" )& ");
-          selectioncom.append(pdbfnum + 1);
-          selectioncom.append(".1)");
-          if (pdbfnum < files.length - 1)
+          if (molsel.length() > 1)
           {
-            selectioncom.append("|");
+            selcom[pdbfnum] = molsel.toString();
+            selectioncom.append("((");
+            selectioncom.append(selcom[pdbfnum].substring(1,
+                    selcom[pdbfnum].length() - 1));
+            selectioncom.append(" )& ");
+            selectioncom.append(pdbfnum + 1);
+            selectioncom.append(".1)");
+            if (pdbfnum < files.length - 1)
+            {
+              selectioncom.append("|");
+            }
+          } else {
+            selcom[pdbfnum] = null;
           }
         }
       }
       for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
-        if (pdbfnum == refStructure)
+        if (pdbfnum == refStructure || selcom[pdbfnum]==null || selcom[refStructure]==null)
         {
           continue;
         }
@@ -582,13 +587,17 @@ public abstract class JalviewJmolBinding implements StructureListener,
         }
         command.append(" ROTATE TRANSLATE;\n");
       }
-      System.out.println("Select regions:\n" + selectioncom.toString());
-      evalStateCommand("select *; cartoons off; backbone; select ("
-              + selectioncom.toString() + "); cartoons; ");
-      // selcom.append("; ribbons; ");
-      System.out.println("Superimpose command(s):\n" + command.toString());
-
-      evalStateCommand(command.toString());
+      if (selectioncom.length() > 0)
+      {
+        System.out.println("Select regions:\n" + selectioncom.toString());
+        evalStateCommand("select *; cartoons off; backbone; select ("
+                + selectioncom.toString() + "); cartoons; ");
+        // selcom.append("; ribbons; ");
+        System.out
+                .println("Superimpose command(s):\n" + command.toString());
+
+        evalStateCommand(command.toString());
+      }
     }
     if (selectioncom.length() > 0)
     {// finally, mark all regions that were superposed.
-- 
1.7.10.2