[Chimera-users] surfnet - separating clefts from cavities

Irene Newhouse einew at hotmail.com
Thu Aug 12 17:02:49 PDT 2010

INGENIOUS!  Makes me embarrassed I didn't think of it!  THANKS!  Not too late - I'll be doing quite a bit of this.
> Subject: Re: [Chimera-users] surfnet - separating clefts from cavities
> From: meng at cgl.ucsf.edu
> Date: Thu, 12 Aug 2010 16:12:41 -0700
> CC: chimera-users at cgl.ucsf.edu
> To: einew at hotmail.com
> Hi Irene,
> Once you've created the Surfnet model,
> (1) split it into separately selectable pieces: Ctrl-click to select the whole model, use command "ac Sc"
> (2) Ctrl-click only the blob of interest to select it. May be hard to get a position that allows this.
> (3) Choose menu item "Select... Invert (selected models)" or equivalently, press right arrow key
> (4) Choose menu item "Actions... Surface... hide"
> Possible alternatives to Surfnet, perhaps of interest:
> (A) Display just the relevant parts of a molecular surface. 
> However, this can be difficult and there are usually ragged edges and extra bits. 
> The parts can be indicated by atomspec in the surface command and/or by using Surface Zone, 
> as in this tutorial section:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html#surfaces>
> (B) Recently I ran across this interesting Web server, Voss Volume Voxelator:
> <http://3vee.molmovdb.org/>
> It makes a "volume" data set (values on a grid) that can be displayed in Chimera as an isosurface 
> occupying pocket and/or channel void space. 
> I tried using the "solvent volume" option with small probe 1.5, large probe 10, high resolution. 
> Opening the output *.mrc file in Chimera and adjusting the isosurface level with the slider in Volume Viewer
> (and using the mesh display style) gave a result similar to Surfnet. 
> One would still need to split this surface model and hide the unwanted blobs as described above.
> Sorry for the delayed reply, I hope not too late,
> 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 Aug 6, 2010, at 1:18 PM, Irene Newhouse wrote:
> > I've been random-walking my way with surfnet, starting from the stand-alone version.
> > I haven't been able to get the output file I need for displaying via RasMol, & while I was
> > googling for cures to that, I discovered the surfnet plugin to Chimera, hurray.
> > I have a protein with several internal cavities, plus many more surface clefts.
> > Has someone worked out an efficient way to display only the internal cavities? 
> > From my previous mucking about with the stand-alone, I already had a 'cavity atoms'
> > pdb-format file which I loaded as model 1 & used that. However, generating the cavity
> > atoms file involved considerable work by hand. At the moment, I can picture
> > splitting the surfaces [using directions in the chimera user archive] & deleting all the
> > surface ones. This is also a fair amount of manual labor - 50 blobs are generated
> > & only 9 are internal. I have other proteins in this family to analyze,
> > & they're probably similar. 
> > Thanks for any advice!
> > Irene Newhouse
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