Hi Doran,
this is a python script, so you must load it with "run".
http://www.pymolwiki.org/index.php/Running_Scripts
Use the "get" command to query default values of settings:
PyMOL>get sculpt_vdw_vis_max
get: sculpt_vdw_vis_max = 0.3
So the complete procedure should look like this:
ru
Hi Thomas,
Thank you for your reply.
I tried running the show_bumps.py script I copied from PymolWiki using
@,however pymol gives me the following error :
NameError: name 'show_bumps' is not defined
How can I define it?
Also, do you know what are the values that sculpt_vdw_vis_max, mid and
min
Hi Arne,
this works for any kind of molecule.
Cheers,
Thomas
Arne Dieckmann wrote, On 05/20/12 22:56:
> Hi Thomas,
>
> is this a general purpose script or does it only work for proteins/amino
> acids?
>
>
> Cheers,
> Arne
>
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Hi Thomas,
is this a general purpose script or does it only work for proteins/amino acids?
Cheers,
Arne
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Dr. Arne Dieckmann
Houk Research Lab | University of California, Los Angeles
On May 20,
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
doran...@post.tau.ac.il wrote,
