JAL-2135 bugfix for error preventing processing of secondary structure annotation...

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 073772a..248cf29 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -82,7 +82,7 @@ public class PDBChain
 
   public PDBChain(String pdbid, String id)
   {
-    this.pdbid = pdbid.toLowerCase();
+    this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
     this.id = id;
   }
 

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 31ed1b7..309e196 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -206,8 +206,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     List<Atom> significantAtoms = new ArrayList<Atom>();
     for (org.jmol.modelset.Atom atom : ms.at)
     {
-      System.out.println("Seq Id : " + atom.getSeqID());
-      System.out.println("To String : " + atom.toString());
+      // System.out.println("Seq Id : " + atom.getSeqID());
+      // System.out.println("To String : " + atom.toString());
       if (atom.isHetero())
       {
         continue;