[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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

...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.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving>

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
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/listen.html#listatoms>

More about attributes here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>

There is also an attributes tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.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 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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