Jules, Right now (and for the foreseeable future) PyMOL's sequence viewer shows actual atoms in an object (whether or not they have coordinates). There isn't currently any way to retrieve that information other than by looking at atoms...
model=cmd.get_model(object-name) for atom in model.atom: print atom.name, atom.chain etc. PyMOL's C code isn't particularly object-oriented -- there is no class which encapsulates the PDB parser. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC 400 Oyster Pt. Blvd., Ste 213 South San Francisco, CA 94080 (650)-346-1154 Fax:(650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Jules Jacobsen > Sent: Monday, October 18, 2004 6:41 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Swissprot > > Hello List, > > I'm trying to make a plugin which will load various features > from a swissprot entry onto a model loaded in PyMol but need > to know a few things such as: > > Where are the sequences of the models stored in pymol and how > do I retrieve them? > > Are these taken from the ATOM or SEQRES sections of the PDB file? > > Is there a PDB parser class somewhere for reading in the PDB files? > > I had a browse through the pymol directory but couldn't find > anything which looked like the above. I'm still very new to > python so the chances are I have missed it. > > many thanks, > > Jules > > > ------------------------------------------------------- > 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 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
