[Chimera-users] volume calculation

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 2 09:10:34 PST 2011

Dear Simone,
(A) If the binding pocket is completely enclosed by the molecular surface:

You can use the Chimera tool "Measure and Color Blobs" (in menu under Tools... Surface/Binding Analysis) to measure the volume and surface area of that surface bubble:

(B) If the binding pocket has one or more openings to the outside surface:

Chimera cannot directly calculate the volume because it does not know where to draw the line (or plane) between pocket inside and outside.  However, it can show pocket volume and area measurements from the CASTp database. CASTp uses Delaunay triangulation and alpha shapes to find pocket boundaries.  If your structure is in the PDB, you can try fetching its CASTp data directly: use Chimera menu "File... Fetch by ID," choose CASTp, and enter the PDB ID code.  That also opens a copy of the structure, so it is best if you start with an "empty" Chimera.

If your structure is not found in the CASTp database, you can go to the CASTp server and request a new calculation for your uploaded structure.  If you request the results to be e-mailed to you, the resulting files can also be displayed in Chimera.

Please see this page for all the details on viewing CASTp information in Chimera:

CASTp server:

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 Dec 2, 2011, at 12:36 AM, sdimicco wrote:

> Dear Chimera developers, 
> is it possible to calculate the volume of the binding site by the softwere? How can I do it?
> Thank you in advance.
> Simone

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