[phenixbb] How to reduce clashscore value

Nathaniel Echols nechols at lbl.gov
Sat Nov 19 08:24:55 PST 2011

On Sat, Nov 19, 2011 at 1:20 AM, Tim Fenn <tim.fenn at gmail.com> wrote:
> However, a purely repulsive potential
> should be able to yield good results!  Perhaps the original poster can try a
> different weighting scheme?

We still haven't heard details from the original poster about the
version used, etc., so it's somewhat premature to draw conclusions
about the causes and/or remedies.  Previous versions of Phenix used a
weight on the repulsive terms that was at least 6x too weak, with the
result that clashscores (and Ramachandran scores) were often
substandard at low resolution.  This has been fixed, and with the
current version it is very rare to see a clashscore above 60 at the
end of refinement *unless* the starting model is severely strained,
and models with good packing are rarely made worse.  With proper
rebuilding and weighting it is entirely possible to refine a sub-4
Angstrom model with Phenix to a clashscore below 20 (the
Molprobity-recommended maximum) without any additional restraints or
tricks.  However, in all of our tests there is a limit to how much
improvement one can expect from minimization alone - and even really
aggressive sampling like what Rosetta does has its limits.  The
geometry restraints aren't the limitation here (Rosetta uses all atoms
and attractive forces too), the optimization techniques are.


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