Jianghai,
Thats correct. To get accessible surface areas for proteins you would
have to use some outside program which can generate SASA points. Using
the rTools interface for PyMOL it should be straightforward to
integrate PyMOL with your SASA program. Check out rTools for PyMOL:
http://www.rubor.de.
Kaushik.
On Tuesday, February 25, 2003, at 01:49 PM, Jianghai Zhu wrote:
Hi, kaushik,
Thanks for the response. Those metheds sound good first, but
when I think about it, they are not real accessible surfaces
because these surfaces still show those small reentrant shapes
between two consecutive atoms. Is there anyway to get around
this? Or can I read any surface file ouput by other programs in
pymol?
Thanks
Jianghai
On Tuesday 25 February 2003 09:56 am, Kaushik Raha wrote:
Hi Jianghai,
Some of these questions have been answered by Warren:
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
- Kaushik.
--
===========================
Jianghai Zhu
Biochemistry & Molecular Biology
Purdue University
Tel: 765-4949249 (O)
765-4633336 (H)
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