[Chimera-users] odd output from surfnet

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 2 16:01:29 PST 2011

I guess it depends on your primary purpose, measurement or display.  The CASTp approach nicely sorts by volume and makes it easy to get which atoms line each pocket.  However, the display of the surface for a pocket is often sub-optimal since Chimera shows surface patches on a per-atom basis (there may be bits of surface shown that don't go with the actual pocket of interest).  These bits don't affect the measurements, however.

If you were able to obtain a blob in the right place with Surfnet, however, that will give a nicer display.  We previously discussed how to hide all the other blobs:

and I forgot to mention that you can get volume and area values for Surfnet blobs using the "Measure and Color Blobs" tool (under Tools... Surface/Binding Analysis).  Note these values can't be compared to the CASTp values since different definitions of surface are used.  A smaller cutoff in Surfnet gives fewer blobs (easier to look through), but may fragment a larger blob that you prefer to remain continuous, so it takes some tinkering which may or may not yield the desired result.

On Mar 2, 2011, at 2:51 PM, Irene Newhouse wrote:

> The stand-alone surfnet did provide lists of cavities; I got sample output when I tried to put the package up. The issue with THAT was that it needs CCCP4, a freeware crystallography package that had, at the time, no 64-bit linux versions & I couldn't get it to install on my system.  Or it can use another hard-to-install-if-you're-on-your-own xtallography package O. There's also hooks into I think Tripos Sybil, [or another popular commercial package, but not the one we've got] but there's no way the boss will spring for that. The author of surfnet has moved on & isn't updating it, so he wasn't much help.  CASTp it is...
> Irene
> > Subject: Re: [Chimera-users] odd output from surfnet
> > From: meng at cgl.ucsf.edu
> > Date: Wed, 2 Mar 2011 14:14:46 -0800
> > CC: chimera-users at cgl.ucsf.edu
> > To: einew at hotmail.com
> > 
> > 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
> > 
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