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