[Chimera-users] surfnet - separating clefts from cavities

Irene Newhouse einew at hotmail.com
Thu Aug 12 18:19:08 PDT 2010

I'm not so bummed that surfnet uses all the atoms -- I can just edit an input pdb file accordingly.
I'll try the volume method & work out saving. Thanks again!
> Subject: Re: [Chimera-users] surfnet - separating clefts from cavities
> From: meng at cgl.ucsf.edu
> Date: Thu, 12 Aug 2010 17:00:24 -0700
> CC: chimera-users at cgl.ucsf.edu
> To: einew at hotmail.com
> Hi Irene,
> Unfortunately surface models aren't directly saved in sessions. 
> Molecular surfaces and volume isosurfaces are effectively saved
> in that they are regenerated from the underlying atomic or volume
> data when the session is restored. Some other surface-generating
> tools are also integrated with sessions, but not Surfnet.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html#whatsaved>
> I should mention that limitation in the docs. Experiments also
> reveal that "Surfnet Selection" is ignoring my atom specification of
> "protein" -- it seems to be using all atoms. However, I can get the
> desired result by using "Surfnet Interface" instead and specifying
> "protein" as both the ligand and receptor. This problem with Surfnet
> Selection is in both the release 1.4.1 and the current daily build, and
> I will be reporting it as a bug.
> If the volume method (alternative (B) in my chimera-users message
> earlier today) had been used, that surface would be restored along
> with the saved session. There is still the drawback that it "forgets"
> it has been split and partially hidden. Upon session restore it is
> regenerated anew and shown in its multiblobbed entirety. Drats,
> foiled again!
> Sorry about that,
> 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 12, 2010, at 4:05 PM, Irene Newhouse wrote:
> > Thanks for your response! I've gone on ahead, manually deleting the clefts. 
> > Also, is there a way to save the computation? When I did a 'save session'
> > & brought it back, the surfnet calculation wasn't there. The calculation itself
> > is quick, it's the hiding the bits you don't want to show that's a pain to regenerate...
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