Neshat,
Warren wrote the surfacing algorithm years ago. A little more discussion on
the algorithm can be found here (
http://www.mail-archive.com/[email protected]/msg07124.html)
and here (http://www.pymolwiki.org/index.php/Get_Area).
Cheers,
-- Jason
On Tue, Nov 12, 2013 at 2:17 AM, neshat haq <[email protected]> wrote:
> Hi,
> I could not find the the algorithm by which pymol calculates the solvent
> ASA.
> What I understood is that pymol adds the vdw radii of atom and probe,
> makes the sphere around the center of selected atoms, puts some dots and
> according to the density of dots it calculates the SASA.
> or it simply uses the Richard & Lee algorithm of rolling water.
> Please clarify my doubts.
> --
> Best regards
> Neshatul Haque
> PhD, Dpt of Biotechnology
> university of hyderabad
>
>
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--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) [email protected]
(o) +1 (603) 374-7120
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