[Chimera-users] Accessible surface area calculation

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 2 09:36:23 PST 2020

Good Morning, Martino Benvenuti!

Surface area (both solvent-accessible, SAS, and solvent-excluded, SES) per atom and per residue is automatically calculated when you display a molecular surface.  For any structure, if you can show the molecular surface, you can see a histogram of the surface area values, color by those values, save them to a file, etc. using "Render by Attribute" (in menu under Tools… Structure Analysis).

You can show a molecular surface with command "surface" or menu Actions... Surface... show. The SES is what Chimera displays, although it gives values for both SAS and SES.  An image here explains the difference:

Use the File menu on the Render by Attribute dialog to save the areaSES and/or areaSAS values per atom or per residue to a file.

To calculate normalized values (% exposure) it would be more complicated, but there are instructions here:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 2, 2020, at 3:29 AM, Martino Benvenuti <mbenvenuti25 at gmail.com> wrote:
> Good morning,
> I would like to know if it is possible to calculate with Chimera the accessible surface area for a selected amminoacid of a protein.
> May you help me to figure it out?
> Thank you for having developed such a great program!
> Have a nice day,
> Martino Benvenuti. 

More information about the Chimera-users mailing list