X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=a9c5f5cb74e1d02cfbf98fc88df835c5bdd46479;hb=cd8070808d46db2a7cdf130c84dbc04c59c20188;hp=e94da73a687c655ee81a5b4a645fb9c21c8ca321;hpb=b879c4a2d32d3489e63ac06917e81637e6bb4068;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index e94da73..a9c5f5c 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -135,8 +135,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
          * see http://wiki.jmol.org/index.php/Jmol_Application
          */
         
-        viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
-                null, "-x -o -n", this);
+        viewer = JalviewJmolBinding.getJmolData(this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
         viewer.setBooleanProperty("defaultStructureDSSP", true);
       } catch (ClassCastException x)
@@ -173,16 +172,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
       {
-        try
+        if (tmpatom.resNumIns.trim().equals(lastID))
+        {
+          // phosphorylated protein - seen both CA and P..
+          continue;
+        }
+        tmpchain = findChain(tmpatom.chain);
+        if (tmpchain != null)
         {
-          tmpchain = findChain(tmpatom.chain);
-          if (tmpatom.resNumIns.trim().equals(lastID))
-          {
-            // phosphorylated protein - seen both CA and P..
-            continue;
-          }
           tmpchain.atoms.addElement(tmpatom);
-        } catch (Exception e)
+        } else
         {
           tmpchain = new PDBChain(getId(), tmpatom.chain);
           getChains().add(tmpchain);