[Chimera-users] Solvent Accessible Surface Area

[Thiruvarangan Ramaraj]

Hi Elaine,

Thanks For your help. 

Just another question, Where are the values for attributes areaSAS and areaSES stored, is there a way to extract these values for the residues and write it to a file.

Thank You

-Thiru

--- On Mon, 9/28/09, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: Solvent Accessible Surface Area
To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
Date: Monday, September 28, 2009, 1:14 PM

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
> I am using Chimera for identifying the surface residues.
> 
> I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers  5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement?
> 
> I just need some help in understanding.
> Thank You
> Sincerely
> -Thiru Ramaraj


Hi Thiru,
In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.  Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.  See for example the GetArea server, which gives "Ratio(%)":
<http://curie.utmb.edu/area_man.html>

However, what Chimera reports is just the surface area of the atom or residue in your structure.  To choose surface residues, I'd probably use a bigger cutoff, say

select :/areaSAS>10

but it depends on what you are going to do with the results.  You can try different values and see what looks reasonable.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco





      
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