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