as anotehr option NACCESS is very simply to run, you can find it here:
http://www.bioinf.manchester.ac.uk/naccess/
hth,
Tommi
On Jan 14, 2011, at 11:36 AM, Fabio Dall'Antonia wrote:
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<beren...@riken.jp>
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<pafon...@gmail.com>
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<beren...@riken.jp>wrote:
------------------------------
Date: Thu, 13 Jan 2011 10:55:51 +0100
From: Tim Gruene<t...@shelx.uni-ac.gwdg.de>
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
Notkestraße 85, Bldg. 25a
D-22603 Hamburg
phone: +49 (0)40 89902-170
fax: +49 (0)40 89902-149
e-mail: fabio.dallanto...@embl-hamburg.de
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
