RE: [PyMOL] CSD .dat files

[DeLano, W. <wa...@su...>]

Charles,

   ".dat" is a hopefully oversubscribed file extension, and the .dat
which PyMOL currently recognizes is for Macromodel.  If you are have
some development skills, consider writing a Python-based CSD file parser
for the Chemical Python portion of PyMOL.  Any ChemPy model can be
loaded straight into PyMOL.  This approach doesn't have quite the
performance as native C reads but, it will suffice for
moderate-throughput applications.

  Example Python code for reading MOL files can be found in
modules/chempy/mol.py.  The code is just over 105 lines and supports
both reads and writes.  One should be able to add a CSD reader with just
an hour or two starting with a description of the CSD file format.  Just
focus on the atom symbols, coordinates, bonds, and bond orders...the
rest can be dealt with later on.

  I propose using the extension ".csd" for csd structure files.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> From: Ross, Charles [mailto:Cha...@st...]
>=20
> I am running latest version (0.73) on an SGI Octane running=20
> IRIX 6.5.14m.
> Structures extracted from the Cambridge Structural Database have the
> extension .dat.  This extension is recognized by PyMol,=20
> although perhaps not
> as a structure file - when I read it, I get no errors, but I get no
> structure either.  Does PyMol recognize CSD structure files,=20
> and if so, what
> is the proper extension?
>=20
> thanks
> Charles Ross
>=20
> Department of Structural Biology
> St. Jude Children's Research Hospital
>=20
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>=20