[Chimera-users] how to measure the volume of the active site

[Elaine Meng]

Hi Thomas,
Chimera can only calculate site volume directly if the pocket is completely enclosed, but for open pockets, Chimera interfaces with the CASTp database of pocket measurements.  If your structure is not already in that database, you can upload it to the CASTp web service to perform the same type of measurements. Results from the server can also be displayed in Chimera if you choose the option to have them emailed to you.

Please see this previous post for details and relevant links:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-December/006981.html>

... except the CASTp server URL is messed up in that post, here is the corrected one:
<http://sts.bioengr.uic.edu/castp/calculation.php>

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 Mar 23, 2012, at 2:54 AM, Thomas Evangelidis wrote:
> 
> Dear UCSF Chimera developers,
> I am interested in measuring the volume of the active site of a kinase. I have searched through the documentation and the only thing I found was how to measure the enclosed volume of a surface object. Is it possible to do what I want with UCSF Chimera? Could you please point me towards the relevant commands?
> Thanks in advance for any help.
> Thomas