[Chimera-users] surfnet - separating clefts from cavities

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 12 17:00:24 PDT 2010

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.

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 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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