// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
pdb = new JmolParser(false, pdbFile, sourceType);
- pdb.addSettings(parseSecStr, parseSecStr, parseSecStr);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)