X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmol.java;h=3df8957d9c01a47f566ce4f72b2abca926ec3853;hb=864c9471858b6995373bea47c10810a1eab1d64b;hp=f5710d34ef5070780b53b49e4b29acbd6316c70d;hpb=6b5be9539790b6a84a9f5f73053f6713ffdba54a;p=jalview.git

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index f5710d3..3df8957 100644
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.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.
  * 
@@ -177,9 +177,10 @@ public class PDBFileWithJmol extends AlignFile implements
                   PDBEntry pdbe = new PDBEntry();
                   pdbe.setFile(getDataName());
                   pdbe.setId(getDataName());
-                  sq.addPDBId(pdbe);
                   pdbe.setProperty(new Hashtable());
-                  pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+                  // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+                  pdbe.setChainCode(String.valueOf(_lastChainId));
+                  sq.addPDBId(pdbe);
                   // JAL-1533
                   // Need to put the number of models for this polymer somewhere for Chimera/others to grab
                   //                  pdbe.getProperty().put("PDBMODELS", biopoly.)
@@ -188,7 +189,10 @@ public class PDBFileWithJmol extends AlignFile implements
                   {
                     String mt = model.getModelTitle() == null ? getDataName()
                             : model.getModelTitle();
-                    mt += _lastChainId;
+                    if (_lastChainId >= ' ')
+                    {
+                      mt += _lastChainId;
+                    }
                     AlignmentAnnotation ann = new AlignmentAnnotation(
                             "Secondary Structure",
                             "Secondary Structure for " + mt, asecstr);