Hi Thomas, 

is this a general purpose script or does it only work for proteins/amino acids? 


Cheers, 
Arne

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
Dr. Arne Dieckmann
Houk Research Lab | University of California, Los Angeles

On May 20, 2012, at 1:15 PM, Thomas Holder wrote:

Hi Doran,

there is a script on the PyMOLWiki that shows VDW clashes:

http://pymolwiki.org/index.php/Show_bumps

There are several sculpt_vdw_vis_* settings which control the visualization:

sculpt_vdw_vis_max
sculpt_vdw_vis_mid
sculpt_vdw_vis_min

Cheers,
  Thomas

doranhen@post.tau.ac.il wrote, On 05/20/12 18:26:
Hi,
I want to make pymol show me clashes between residues vdw spheres only  
if the clashes are above a certain clash cut off, say if the clashing  
residues overlap by x square angstrom than its o.k, but if they  
overlap by more then x it's should show as a clash.
Does anyone know of a way to do it in pymol?

Thank you,
Doran

--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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