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<[log in to unmask]>
>> 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<[log in to unmask]>
>> 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<[log in to unmask]>wrote:
>>
>> ------------------------------
>>
>> Date: Thu, 13 Jan 2011 10:55:51 +0100
>> From: Tim Gruene<[log in to unmask]>
>> 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: [log in to unmask]
>
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
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