+ 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);
+ }