Dear all,
I would like to know if there is a way to measure between surfaces
(actually two parts of one surface) in pymol or another program. We would
like to measure the active site of our enzyme structure, and noticed that
authors of related structures had done this type of measurement with GRASP
surfaces.
I apologize if this question is too simple, since I am still not that
familiar with all of pymol's facilities.
Thank you for any suggestions,
Jim
-----Original Message-----
From: Robert Campbell <robert.campb...@queensu.ca>
To: pymol-users@lists.sourceforge.net
Date: Thu, 22 Nov 2007 16:56:01 -0500
Subject: Re: [PyMOL] obtaining coordinates of solvent-surface points
> Hello John,
>
> On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ <josh8...@yahoo.com>
> 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
> <robert.campb...@queensu.ca>
> http://pldserver1.biochem.queensu.ca/~rlc
>
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