Hello,
I have found that, in many cases, switching on the Lennard-Jones restraint (energy_data.dynamic_lennard = True) and up-weighting it with respect to other restraints (env.schedule_scale...) can reduce the bad van der Waal's interactions as measured by Molprobity.
Cheers,
Nick
On 20 November 2010 13:03, Anton Iershov <" target="_blank">a.yershov@yahoo.com> wrote:
Dear Modeller Caretaker, When performing homology modeling with default parameters ("model-default.py") and subsequent analysis with Molprobity (http://molprobity.biochem.duke.edu/) I obtain models with much more high clashscore than the template has, and model optimization does not help much. Then, Kinemage (http://kinemage.biochem.duke.edu) shows a lot of "bad" van der Waals contacts. What should I do to obtain model of higher quality (I mean to reduce clashscore and number of "bad" contacts)?
Thanks in advance, Anton.
---------------------- Dr N M Burton Department of Biochemistry University of Bristol BS8 1TD, UK +44 117 3312149 nick.burton@bristol.ac.uk