Rene wrote: > What still confuses me is how the viewer knows which AtomSetIndex to > use to get the AtomSetName (through the JmolAdapter) in the case of a > pdb file, since the real AtomSetIndex associated with a particular atom > may be lost.
I am not sure exactly what your question is. Let's try this: The JmolAdapter provides: getAtomSetCount() getAtomSetNumber(atomSetIndex) getAtomSetName(atomSetIndex) getAtomSetProperties(atomSetIndex) each atom has an atomSetNumber associated with it. Atoms display based upon their atomSetNumber. > On an aside, the atomSetNumber for an atom in a pdb file does not > associate it with a particular frame in an animation as it obviously > does for something like the NWChemReader? A model in a pdb file and a frame in a NWChem file are the same. Each atom has a model number associated with it. At render time, the atoms know whether or not they should be rendered by looking at the displayedModelNumber. Miguel ------------------------------------------------------- This SF.net email is sponsored by: IT Product Guide on ITManagersJournal Use IT products in your business? Tell us what you think of them. Give us Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more http://productguide.itmanagersjournal.com/guidepromo.tmpl _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
