+ if (pdbFile != null && isCIFFile(pdbFile))
+ {
+ pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
+ secStructServices, pdbFile, protocol);
+ }
+ else
+ {
+ pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
+ pdbFile, protocol);
+ }
+
+ if (pdb.getId() != null && pdb.getId().trim().length() > 0