RE: [PyMOL] Surface and SASA

[DeLano, W. <wa...@su...>]

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=3Dvdw+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:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Kaushik Raha [mailto:kx...@ps...]
> Sent: Friday, February 07, 2003 4:37 PM
> To: pym...@li...
> Subject: [PyMOL] Surface and SASA
>=20
>=20
> 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.
>=20
> 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?
>=20
> Thanks in advance.
>=20
> Kaushik Raha
> Penn State University.
>=20
>=20
>=20
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