Re: [modeller_usage] high model clashscore

[Nick Burton <>]

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">> 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