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/pymol-users@lists.sourceforge.net/msg00359.html http://pymolwiki.org/index.php/Molecular_Sculpting Cheers, Thomas On 25 Nov 2013, at 14:40, Lapolla, Suzanne M (HSC) <suzanne-lapo...@ouhsc.edu> 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 ------------------------------------------------------------------------------ Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
