Kaushik,
Good questions.
(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
representations:
for dots:
show dots
set dot_mode,1
set dot_density,3
for spheres:
alter all,vdw=vdw+1.4
show spheres
(NOTE that after the alter command, the other surface representations will be
invalid -- also note that you may need to "rebuild" after using alter.)
(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
load prefix.prm
load_traj 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.
help load_traj
for more information.
Cheers,
Warren
--
mailto:[email protected]
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
> -----Original Message-----
> From: Kaushik Raha [mailto:[email protected]]
> Sent: Friday, February 07, 2003 4:37 PM
> To: [email protected]
> Subject: [PyMOL] Surface and SASA
>
>
> Maybe this has already been discussed but I was wondering if the
> surface that PyMOL generates is solvent accessible surface
> area (SASA)
> ? If so what is the solvent probe radius? The reason I ask is some
> atoms seem to have exposed surfaces when rendered with PyMOL
> whereas my
> SASA program has it as non-exposed.
>
> Another question I have is does PyMOL read AMBER topology (prmtop)
> 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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