Sergio, As is typical with PyMOL, the secondary structure assignment engine is ad hoc and empirically tuned to produce desirable aesthetics. Though there are some phi/psi's that are clearly helix/sheet and others that are clearly not, there are certain regions of phi/psi space were the assignment is subjective or arbitrary. In my experience, algorithms based on strict definitions tend to blow it in such regions, and so PyMOL's algorithm is "fuzzy" in that there is a grey area where residues may be accepted or rejected as helix/sheet depending upon the surrounding context.
So to answer your question, there aren't any hard & fast definitions. But you are welcome to check out the collection of settings beginning with "ss_helix" and "ss_strand", noting that the include and exclude settings are devations around the target in degrees. If you think PyMOL is botching an assignment, then you might try varying these. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Sergio E. Wong > Sent: Sunday, June 05, 2005 12:31 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] definitions of secondary structure > > Dear sirs; > > I'm wondering what are the definitions employed to > determine secondary structure in pymol. Specifically, what > is the variation allowed from ideal beta strand or alpha > helical phi/psi angles?? Thanks > > -Sergio > > > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far > can you shotput a projector? How fast can you ride your desk > chair down the office luge track? > If you want to score the big prize, get to know the little guy. > Play to win an NEC 61" plasma display: > http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
