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.
On Monday, February 24, 2003, at 09:46 PM, Jianghai Zhu wrote:
Hi,
When I used "show surface, protein", what kind of surface did I
generate? Molecualr surface, accessible surface (what is the
probe radius?)? How can I define the type of surface I want and
the probe radius? Besides generating the surface by itself,
could pymol read other surface files? like msms format, grasp
format, etc.
Thanks.
Jianghai
--
===========================
Jianghai Zhu
Biochemistry & Molecular Biology
Purdue University
Tel: 765-4949249 (O)
765-4633336 (H)
===========================
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