[Molvis-list] Exporting molecular surfaces

Vikberg, Gunnar vikbergg at msoe.edu
Thu Jun 9 11:53:18 EDT 2005

Hi Bathsheba Grossman,
Along with Dr. Elmar Krieger's tips on using Yasara, there is a program that uses GRASP (not GRASS) surfaces directly and is able to create high resolution renderings of them. The program is called POV4GRASP, and can be found at http://pov4grasp.free.fr/ with source code also available for download. If you're using GRASP on an SGI machine, this is possibly an easy way to go.
Furthermore, GRASP is able to generate higher resolution images by changing the default probe size. This is done in the SET PARAMETERS menu, where you can find the PROBE RADII VALUES option. A smaller probe radius should generate a higher resolution mesh. You can find the explanation for this in the GRASP manual (http://honiglab.cpmc.columbia.edu/grasp/grasp_contents.html#set_params).
I hope this helps,
Gunnar Vikberg


From: molvis-list-bounces+vikbergg=msoe.edu at bioinformatics.org on behalf of Elmar Krieger
Sent: Thu 6/9/05 1:48
To: Molecular Visualization, especially in education with freeware
Subject: Re: [Molvis-list] Exporting molecular surfaces

Hi Bathsheba,

One way to get a hi-resolution molecular surface in .pov format:
- Download YASARA View ( http://www.yasara.org )
- Download Michel Sanner's MSMS program from
www.scripps.edu/~sanner/python/packager.html and make sure that the MSMS
executable can be found in the directory yasara\sms
- Run YASARA and load your PDB file
- Click on View > Show surface > Parameters, select the highest resolution and
toggle 'Analytic surface using MSMS'.
- Click View > Show surface > All
- Click File > Save as > Ray-traced screenshot > Create PovRay scene description

There are many options to color your surface and adjust transparencies of outer
and inner surface sides, the vertices can also inherit the color of the closest

Good luck,

Elmar Krieger, PhD
YASARA Biosciences & CMBI Outstation Austria
Neue-Welt-Hoehe 13/b
A-8042 Graz

=WHAT IF YASARA knows the answer?!=
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