[Chimera-users] Cavities

[Elaine Meng]

On Jan 12, 2011, at 5:04 AM, Beale, John wrote:

> Is it possible to find cavities in a protein structure using Chimera?

Hi John,
There are at least two approaches connected with Chimera, CASTp and Surfnet.

CASTp is a database with pre-computed pocket areas and volumes for many (most?) PDB entries.  You can fetch CASTp data directly into Chimera, for example by choosing menu entry "File... Fetch by ID" and then indicating CASTp database and giving a PDB ID code.  Don't open the structure beforehand, as it will open automatically along with the results.  If the structure you are interested in is not in that database, you can go to the CASTp Web site and upload your structure for a calculation, and it can send you the results back by e-mail.  Then you can open the results in Chimera.  Details on using CASTp data in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>

There is also a tool in Chimera called Surfnet (under Tools... Surface/Binding Analysis) that calculates surface blobs filling cavities. In my experience, it may require some experimentation with parameter settings to get blobs in the expected locations, however.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html>

I've also used some Web servers separate from Chimera, but then used Chimera to display the results:

3V: Voss Volume Voxelator (I tried the "Solvent Extraction" option to find cavities)
<http://3vee.molmovdb.org/>

MolAxis server
<http://bioinfo3d.cs.tau.ac.il/MolAxis/>

... and here is a Chimera Image Gallery entry showing both CASTp and MolAxis results for a potassium channel, and describing how to alter MolAxis results for display in Chimera:
<http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco