try
{
- if (pdbFile != null && isCIFFile(pdbFile))
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ if (isParseWithJMOL || (pdbFile != null && isCIFFile(pdbFile)))
{
pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
secStructServices, pdbFile, protocol);
}
ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
+ if (isMapUsingSIFTs && seq.isProtein())
{
setProgressBar(null);
setProgressBar(MessageManager