JAL-1919 basic support for importing and viewing mmCIF files - mapping support not...

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 58611e2..f7eba09 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -309,16 +309,19 @@ public class PDBfile extends jalview.io.AlignFile
       // TODO: decide if we should dump the datasource to disk
       entry.setFile(getDataName());
     }
-    pdbSequence.addPDBId(entry);
 
     DBRefEntry sourceDBRef = new DBRefEntry();
     sourceDBRef.setAccessionId(id);
     sourceDBRef.setSource(DBRefSource.PDB);
     sourceDBRef.setStartRes(pdbSequence.getStart());
     sourceDBRef.setEndRes(pdbSequence.getEnd());
-    pdbSequence.setSourceDBRef(sourceDBRef);
+
     // PDBChain objects maintain reference to dataset
     SequenceI chainseq = pdbSequence.deriveSequence();
+    chainseq.setSourceDBRef(sourceDBRef);
+    chainseq.addPDBId(entry);
+    chainseq.addDBRef(sourceDBRef);
+
     seqs.addElement(chainseq);
 
     AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
@@ -383,7 +386,7 @@ public class PDBfile extends jalview.io.AlignFile
   {
     try
     {
-      Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+      Class cl = Class.forName("jalview.ext.jmol.JmolParser");
       if (cl != null)
       {
         final Constructor constructor = cl