[Chimera-users] Binding Pocket Internal Volume Calculation

[ppwanjari]

Hi Elaine,
Thanks a lot. I got the required volume using Surfnet. The calculated volume
is close to expected value.

-Piyush

On Wed, Mar 24, 2010 at 11:07 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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>
>
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