Hi Francois,
I have been using MSMS (Sanner et al., 1996) quite a lot, one feature
that I like about it is the output of per-atom area values, what is
exactly the thing you want. Areas of both the solvent-accessible and the
solvent-excluded surface (SES) are computed and written to a file
(.area) if MSMS is run with the -af switch, while to my knowledge the
numerically calculated triangulated surface files (.vert, .face) are
based on the SES by default.
I seem to recall that I once compiled MSMS from source, but I might be
wrong. Looking onto the MSMS page on the Scripps site,
http://mgltools.scripps.edu/packages/MSMS/ there are apparently only
precompiled binaries by now.
Regards,
Fabio
Date: Thu, 13 Jan 2011 15:00:54 +0900
From: Francois Berenger<[email protected]>
Subject: What is the simplest method to analytically compute the
Solvent-Accessible Surface Area of a given atom in a protein?
Hello,
Does someone know some good articles on this particular topic?
I'd like to implement the thing myself, however if there is
a good software doing the job (with readable source code),
I might use and cite it.
Best regards,
Francois.
------------------------------
Date: Wed, 12 Jan 2011 22:30:55 -0800
From: Pavel Afonine<[email protected]>
Subject: Re: What is the simplest method to analytically compute the
Solvent-Accessible Surface Area of a given atom in a protein?
Bulk-solvent mask calculation (if that's what you want) is available in
CCTBX library, and it can be easily used. Let me know if interested and we
can discuss it off-list. I can send you some ten-line Python script-example
that computes it given a PDB file.
Pavel.
On Wed, Jan 12, 2011 at 10:00 PM, Francois Berenger<[email protected]>wrote:
------------------------------
Date: Thu, 13 Jan 2011 10:55:51 +0100
From: Tim Gruene<[email protected]>
Subject: Re: What is the simplest method to analytically compute the
Solvent-Accessible Surface Area of a given atom in a protein?
Dear Francois,
my starting point would be 'man areaimol' which also contains the references
REFERENCES
1. B.Lee and F.M.Richards, J.Mol.Biol., 55, 379-400 (1971)
2. E.B.Saff and A.B.J.Kuijlaars, The Mathematical Intelligencer, 19,
5-11 (1997)
http://www.math.vanderbilt.edu/~esaff/texts/161.pdf
Cheers, Tim
--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
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