On May 12, 2011, at 4:00 PM, CCP4BB automatic digest system wrote:
Hey all,
I would like to introduce point mutations in a structure and quickly
(and dirtily) minimize the new residue. (Best rotamer dependent on
local environment, or the like.) What are simple approaches that
don't
involve VMD/NAMD or some such overkill.
Chimera is pretty good for this. It has a Rotamer tool for making the
substitution based on Dunbrack or Richardson libraries, and can screen
based on probability / H-bonds formed / steric clashes:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/rotamers.html
You can then use Chimera's Minimize Structure tool to minimize the
side chain and/or the local environment or, if you're feeling frisky,
the whole protein:
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/minimize/minimize.html
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
Chimera home page: www.cgl.ucsf.edu/chimera
