[Chimera-users] solvent-accessible surface area

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 2 12:14:41 PST 2013


Hi Amit,
Your message did go to the list  (you just emailed the address chimera-users at cgl.ucsf.edu)!!

I don't know of any standard, commonly used surface area value to use as the cutoff between buried and exposed.  Often people will use a percentage normalized by the area of that same amino acid type in some model of the completely exposed state.  For example, they might decide that an amino acid is buried if its surface area in the protein is less than 10% of the surface area of that same type of amino acid in a Gly-X-Gly tripeptide.  However, Chimera does not do such a normalization, nor provide surface areas of completely exposed states.  You either have to use your own judgement as to what surface area cutoff you want to use, or use some other program such as getArea that does provide normalization:
<http://curie.utmb.edu/area_man.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 28, 2013, at 4:52 PM, "Amit Goyal" <amitgsir at gmail.com> wrote:

> Hi Elaine,
> Today I subscribe to Chimera mailing list, but unable to get the proper way to post a query on it. So I am sending the query this way.
>  
> I have been reading this post about how to get the areaSAS and areaSES values for any residues.
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002617.html
>  
> Still, I think, is there any specific values/range for the areas AS to decide whether a particular amino acid residues is buried or exposed to the solvent.
> Hoping for 
> Thanks for your help.
> Sincerely, 
> AMIT




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