Hi Edmund,
Actually, PyMOL uses a set of stored coordinates for fragments
and residues. They can be found in $PYMOL_PATH/data/chempy/fragments.
The files have .pkl extensions, which stands for pickled chempy model.
These files can be viewed directly in PyMOL, or can be introspected by
unpickling them in a Python interpreter.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (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 Edmund Kump
> Sent: Wednesday, September 17, 2003 3:49 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] modifying atom coordinates
>
> Greetings,
>
> I am interested in modifying how pymol generates the coordinates of
> atoms in a peptide chain as you add residues to it. I am an
> undergraduate math student, so my knowledge in this area is in the
> range of "nothing". I would assume that this would be in the bonding
> or editor modules, but so far I haven't found what I'm looking for. In
> what Chempy or Pymol module(s) can I find the code that determines
> these coordinates?
>
> Thanks,
> Edmund Kump
> ek...@mathlab.sunysb.edu
> Applied Mathematics and Statistics
> SUNY Stony Brook
>
>
>
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