[Chimera-users] Binding Pocket Internal Volume Calculation
ppwanjari at gmail.com
Wed Mar 24 14:31:44 PDT 2010
Thanks a lot. I got the required volume using Surfnet. The calculated volume
is close to expected value.
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.
> 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 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.
>> 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
>> CASTp server:
>> I hope this helps,
>> 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.
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
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