(1) PyMOL doesn't show the solvent accessible surface, rather it shows =
the solvent/protein contact surface. The solvent accessible surface =
area is usually defined as the surface traced out by the center of a =
water sphere, having a radius of about 1.4 angstroms, rolled over the =
protein atoms. The contact surface is the surface traced out by the vdw =
surfaces of the water atoms when in contact with the protein.
PyMOL can only show solvent accessible surfaces using the dot or sphere =
(NOTE that after the alter command, the other surface representations =
will be invalid -- also note that you may need to "rebuild" after using =
(2) PyMOL can load amber trajectory files if you have a matching prmtop =
to go with the trajectory. Here's how:
a. name your prmtop file prefix.top
b. name your trajectory prefix.trj
"prefix" can be whatever you want it to be, but they must match for both =
files, unless you specify an alternate object name.
for more information.
Warren L. DeLano, Ph.D.=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
> -----Original Message-----
> From: Kaushik Raha [mailto:kxr205@...]
> Sent: Friday, February 07, 2003 4:37 PM
> To: pymol-users@...
> Subject: [PyMOL] Surface and SASA
> Maybe this has already been discussed but I was wondering if the=20
> surface that PyMOL generates is solvent accessible surface=20
> area (SASA)=20
> ? If so what is the solvent probe radius? The reason I ask is some=20
> atoms seem to have exposed surfaces when rendered with PyMOL=20
> whereas my=20
> SASA program has it as non-exposed.
> Another question I have is does PyMOL read AMBER topology (prmtop)=20
> files? And how do I load it and read it along with a crd file?
> Thanks in advance.
> Kaushik Raha
> Penn State University.
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