[Chimera-users] Using Surfnet tool in a per-frame python script

William McDonald pchem at ucsc.edu
Wed Jul 31 16:12:54 PDT 2013

Dear Chimera Developers,

First, thank you all for such a wonderful program! Also, thanks to the
users' list for such quick, thorough, and always-helpful answers!

Second, a little background: I have a gromacs MD simulation (well several,
actually) of a small ligand diffusing through a protein. Because the ligand
requires the entire simulation to traverse the protein cavity, I was
thinking of using the Surfnet tool to accumulate or "build-up" the cavity
interface between the ligand and protein using a per-frame python script a
la Eric's suggestion in the Dec 2009 [Chimera-users] Surfnet command line
thread on this mailing list. I was thinking I could then "prune" the
accumulated SurfaceModel using the surfvol.py script available on the
http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts download page.

Now, I can generate a Surfnet surface easily (as Eric points out) for each
MD frame using the python commands

from Surfnet import interface_surfnet

But how, if possible, can I combine all the individual SurfaceModels into
one surface? Also, and not secondarily, does this seem like a reasonable
approach to obtain the ligand-protein cavity surface?

Thanks again for all your generous support.
William J. McDonald
Postdoctoral Scholar
Department of Chemistry and Biochemistry
University of California, Santa Cruz
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