Re: [PyMOL] resubmitting vanderwaal bumps ?

Hi Suzanne,

the showbumps.py script uses the sculpting mechanism, which is no real energy forcefield and thus those units are arbitrary.

Calculating the stability of a mutant is a very advanced task, and PyMOL is not made for that. PyMOL can give you visual clues for your reasoning, like obvious vdw clashes.

A tool that I've used in the past to calculate mutant ddG: http://foldx.crg.es/
There are of course others, like ROSETTA, or MD simulations.

For sculpting, see also:
http://www.mail-archive.com/pym...@li.../msg00359.html
http://pymolwiki.org/index.php/Molecular_Sculpting

Cheers,
  Thomas

On 25 Nov 2013, at 14:40, Lapolla, Suzanne M (HSC) <suz...@ou...> wrote:

> I noticed my question was truncated when I submitted it so will try again.
> When I run showbumps.py on Pymol I get a vanderwaal value of about 163.
> I need a good ref point as to what that number represents.
> Thanks, Suzanne