[Chimera-users] Binding Pocket Internal Volume Calculation

[ppwanjari]

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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