From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 4 Dec 2012 10:48:53 +0000 (+0000)
Subject: JAL-674 commented out annotate3d calling code for Jmol external processing routine
X-Git-Tag: Jalview_2_9~221^2^2~8^2~21
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9b46450418018dbd0cbd94640af65367a3fa1126;p=jalview.git

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 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");