X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=1d95f40a52af8f15a33f037ebdbbe6cecedf5ea0;hb=9b46450418018dbd0cbd94640af65367a3fa1126;hp=99d55b02b7e7db63d499ad2fff1c6dd065aa4c6c;hpb=7d00e99455868f5895682506e495d4e12e8c2fc2;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 99d55b0..1d95f40 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -227,10 +227,8 @@ 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");