X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=148f252870edbbf3eb9cdce60d2ae1170483d4f6;hb=1ae9824ef37ce4ed36d1da986003474b47d1ab11;hp=4afc526322b4ea52b680f8a3dbba890cca809668;hpb=b13f521553582ef2fbfd7815ae25e23284babdea;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 4afc526..148f252 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,13 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
@@ -30,13 +37,6 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
 /**
  * Routines for generating Chimera commands for Jalview/Chimera binding
  * 
@@ -121,6 +121,7 @@ public class ChimeraCommands
         final Map<String, List<int[]>> modelData = colourData.get(model);
         for (String chain : modelData.keySet())
         {
+          boolean hasChain = !"".equals(chain.trim());
           for (int[] range : modelData.get(chain))
           {
             if (!firstPositionForModel)
@@ -135,7 +136,10 @@ public class ChimeraCommands
             {
               sb.append(range[0]).append("-").append(range[1]);
             }
-            sb.append(".").append(chain);
+            if (hasChain)
+            {
+              sb.append(".").append(chain);
+            }
             firstPositionForModel = false;
           }
         }