Re: [PyMOL] obtaining coordinates of solvent-surface points

[Robert C. <rob...@qu...>]

Hello John,

On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ <jos...@ya...>
wrote:

> Hello:
> Im new at pymol and would like to obtain the
> coordinates of the dots that make up the
> solvent-accessible surface.  I can obtain the vertices
> using cmd.get_povray()[1], but that will give me a
> list of coordinates of open cylinders with spheres at
> either end.  Perhaps these sphere and cylinders are so
> small that I could use any of them as the coordinates
> for the surface dot. Or, would it be more exact to use
> the midpoint of the cylinder?  Any suggestions?

Rather than use PyMOL's surface, I've used the triangulated surface output
by Michel Sanner's msms program.  I've written a few python scripts that
allow various manipulations.  Just today, in fact, I wrote a script to
calculate surface areas from within PyMOL.  I also have previously
written some python code that does a calculation similar to the CCP4
program "sc" (surface complementarity).  This allows me to colour the
surface of, for example, an inhibitor according to how complementarity
it is to an enzyme active site.  I hadn't added these to my PyMOL scripts
web page, but I will do so now.  Look for "msms_pymol.py" at

  http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Of course, one needs to obtain msms, but that can be simply found at

  http://mgltools.scripps.edu/downloads

The msms_complementarity calculation is done outside pymol and the
resulting vertex and triangle files are read by a separate script to create
a CGO representation of the msms surface.  I'll get those up on the web
site tomorrow, perhaps.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc