Re: [Chimera-users] surfnet - separating clefts from cavities
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...
On Aug 12, 2010, at 5:00 PM, Elaine Meng wrote:
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!
I must further note that for the session to restore, one must also keep the volume data file around (the *.mrc file in this case), it is not included in the session file. Elaine
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! Irene
Subject: Re: [Chimera-users] surfnet - separating clefts from cavities From: meng@cgl.ucsf.edu Date: Thu, 12 Aug 2010 17:00:24 -0700 CC: chimera-users@cgl.ucsf.edu To: einew@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...
participants (2)
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Elaine Meng -
Irene Newhouse