[Chimera-users] surface area calculations

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 4 10:10:16 PDT 2014

Dear Bhaskar,
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.

More information about the Chimera-users mailing list