From: Sergio E. Wong <swon9@it...> - 2005-06-05 07:30:54
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
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.
Warren L. DeLano, Ph.D.
. 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
> -----Original Message-----
> From: pymol-users-admin@...
> [mailto:pymol-users-admin@...] On Behalf Of
> Sergio E. Wong
> Sent: Sunday, June 05, 2005 12:31 AM
> To: pymol-users@...
> 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
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