[Chimera-users] Binding Pocket Internal Volume Calculation

[Elaine Meng]

Hi Piyush,
Chimera can only calculate the volume of a pocket that is completely  
enclosed, whereas CASTp figures out where the "tops" of open pockets  
are, allowing calculation of their volumes.  The only other  
possibility in Chimera is to use the Surfnet tool (under Tools...  
Surface/Binding Analysis) to try to create a surface blob where you  
think the pocket in your structure lies.  Then you can use the  
"Measure and Color Blobs" tool (under Tools... Surface/Binding  
Analysis) to measure the volume enclosed in that blob.

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

In my experience, however, it is not easy to get exactly the blob you  
want by adjusting the Surfnet parameters.  Another caveat is that the  
values may not be strictly comparable to those from other approaches  
(CASTp etc.) because the methodology is different.

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, 2010, at 4:30 PM, ppwanjari wrote:

> Hi Elaine,
> Thanks for your last reply.
> Actually, I am trying to understanding volume of host-guest  
> structures similar to that of receptor-ligand. So, using the first  
> option (Measure Volume and Area), I obtained vdw volume for guests.
> But, for predicting the volume of pocket of host (similar to  
> receptor), I loaded the .pdb into CASTp server, but its not  
> selecting proper region. Instead of pocket atoms its selecting few  
> atoms present at the below the pocket. So, its not giving me the  
> correct volume of pocket. Can we manually select the atoms of pocket  
> to find the inside volume? Otherwise I guess, I need to write a code  
> for it.
>
> Thank You.
> Piyush
>
>
> On Mon, Mar 22, 2010 at 10:56 AM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>
>
> CASTp server:
> <http://sts-fw.bioengr.uic.edu/castp/calculation.phphttp://sts-fw.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 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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