[Chimera-users] Binding Pocket Internal Volume Calculation

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 22 08:56:06 PDT 2010

Hi Piyush,
I see two related calculations.
(1) If you have a ligand molecule, you can just show its molecular  
surface and then measure the volume inside that surface.  Display the  
molecular surface of that molecule, then choose Tools... Volume  
Data... Measure Volume and Area.  Make sure you have chosen the right  
surface in that dialog, if more than one exists.

(2) The other calculation is on the receptor structure.  For that,  
Chimera can show pocket volume and area measurements from the CASTp  
database. If your structure is in the database, you can just call up  
the results in Chimera.  For example, choose 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 in that 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 Mar 21, 2010, at 3:25 PM, ppwanjari wrote:

> Hello Everyone,
> I want to determine the inside volume of a pocket shaped molecule.  
> Does anyone know how can I do it with Chimera? I am only able to  
> measure volume of pocket-making atoms with Chimera, but not the  
> inside volume.
> Thanks.
> Piyush

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