[Chimera-users] Solvent Accessible Surface Area

[Elaine Meng]

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