[Chimera-users] surface area calculations
meng at cgl.ucsf.edu
Fri Apr 4 10:10:16 PDT 2014
As explained in more detail here:
...when you show a molecular surface in Chimera (e.g. menu: Actions... Surface... show) it will automatically calculate solvent-accessible surface (SAS) and solvent-excluded surface (SES) areas. The total is reported in the Reply Log (in Favorites menu), but also per each atom and each residue. The per-atom and per-residue area values are attributes named areaSAS and areaSES.
In the Render/Select by Attribute tool (menu "Select... By Attribute Value" or "Tools... Depiction... Render by Attribute"), you can: see a histogram of the values, select or color atoms by the values, or (using its File menu) write a text file with the values.
Or, to report per-atom values in the Reply Log instead of writing a file, you could use the "list atoms" command, for example:
list atoms attribute areaSAS
More about attributes here:
There is also an attributes tutorial:
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Apr 4, 2014, at 8:33 AM, Bhaskar Bagchi wrote:
> Respected Sir
> I want to calculate surface area of different atoms in a molecule. Is it possible in chimera? Please help me.
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