[Chimera-users] Splitting surfnet surfaces and calculate enclosed volume.

[Elaine Meng]

On Mar 26, 2008, at 11:12 AM, Jean-Didier Maréchal wrote:
> Hi everyone,
> I would like to calculate the volume of the main pocket provided by a
> surfnet calculation performed on a given selection. The resulting
> calculation returns me different pockets of variable sizes. And I have
> two small questions:
>
> 1. Is there a way to split the resulting surfaces in individual size
> ranked entities so that I can calculate the volume of each of them?
> 2. What would be the easiest way to call the mv accelerator function
> from the python shell (whether by a command emulation or a directly
> importing a module)?
> Cheers,
> JD


Hi JD,
In recent versions of Chimera (newer than the production release in  
November 2007... get a daily build), you can measure the surface area  
and enclosed volume of each separate "blob" with "Measure and Color  
Blobs":

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/ 
pickblobs.html

It doesn't give you a ranked list, however; you just have to click on  
each blob you want to measure.  The surface area and volume are  
computed directly from the surface triangle positions.

I should mention the new "CASTp fetch" capability: it looks up a  
structure in the CASTp database and brings up a table of all the  
pockets, their surface areas and volumes, and pocket mouth  
measurements.  It is most excellent, the main limitation being that  
not all PDBs are in that database.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html

You can fetch from CASTp with File... Fetch by ID, or with a command  
such as:

open castp:4enl
open castp:2gsh.A

(the latter showing how to get results for just a particular chain).

I will have to leave question #2 to someone else!  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html