[Chimera-users] surfnet - separating clefts from cavities

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 12 16:12:41 PDT 2010

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:

(B) Recently I ran across this interesting Web server, Voss Volume Voxelator:
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 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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