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)
===========================
