[Chimera-users] odd output from surfnet

[Elaine Meng]

Hi Irene,
I am not certain if anything is wrong, it may be the way that Surfnet works.  In my own experience, it's difficult to generate the desired "blob" with Surfnet and to pick it out from the many other small blobs.

Personally I prefer to use CASTp.  If your structure is not in the CASTp database (you could try Open... Fetch by ID in the Chimera menu to check) you can submit it to the CASTp web server, receive the results by email, and then display them in Chimera if you like.  The cavities are listed in a dialog in order of decreasing size and other information, such as number of openings.

Viewing CASTp info in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>

CASTp server:
<http://sts-fw.bioengr.uic.edu/castp/calculation.php>

These additional web servers may also be of interest...
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/>
see also for display in Chimera,
<http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/cavities/cavities.html>

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 2, 2011, at 1:16 PM, Irene Newhouse wrote:

> I'm trying to get an image of channels in the attached protein. It's actually a dimer, & the surfaces looked bizarre for the dimer, so I thought maybe surfnet was choking on the repeated residue numbers when you use chain ID, so I clipped it down to the monomer. That' still odd. I've attached a png of the result, using the defaults, & the pdb file of the monomer.  What am I doing wrong? Is there a way to get the n largest channels, instead of all of them?
> 
> Thanks!
> Irene Newhouse