JAL-674 commented out annotate3d calling code for Jmol external processing routine

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 8a826a1..6a61f6a 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -235,10 +235,8 @@ public class PDBfile extends jalview.io.AlignFile
   }
   private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
   {
-//    System.out.println("this is a PDB format and RNA sequence");
-    Annotate3D an3d = new Annotate3D();
-    AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
-    replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+    // process prot sequence with Jmol to get annotated alignment. 
+    // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
   }
   private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
 //    System.out.println("this is a PDB format and RNA sequence");