[phenixbb] How to reduce clashscore value

Tim Fenn tim.fenn at gmail.com
Sat Nov 19 01:20:14 PST 2011

On Fri, Nov 18, 2011 at 1:15 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> **
> 1) the weighting between the chemical and X-ray potentials is putting too
> much emphasis on the data (see http://dx.doi.org/10.1107/S0907444911039060
> )
> most of the time the default weight used in Phenix is good enough. Once
> it's not the case, then you can always use "optimize_xyz_weight=true" to
> get the optimal value. This is described in details here:
> http://www.phenix-online.org/newsletter/
> see article "Improved target weight optimization in phenix.refine".
The method of using the ratio of gradients doesn't make sense in a maximum
likelihood context, and I've never understood the rationale for it - even
this paper notes that it breaks down at high/low resolution regimes (as
would be expected, since the X-ray gradient will be very large/small,

2) I'm not sure what kind of vdW function phenix uses by default (repulsive
> only?), but its very difficult, if not impossible, to get accurate
> interatomic separation distances without summing a Lennard-Jones style vdW
> potential and (at least) fixed atomic charge electrostatics.
> phenix.refine uses repulsion term only. Although one can imagine reasons
> why attraction terms may be helpful, in reality they may be
> counterproductive if the model geometry quality is not great since
> attractive terms may lock wrong conformations and not let them move towards
> correct positions dictated by the electron density.
Refinement using a force field without electrostatics versus with
electrostatics was recently investigated (
http://dx.doi.org/10.1021/ct100506d), and found to favor its inclusion
across a range of models/resolutions.  However, a purely repulsive
potential should be able to yield good results!  Perhaps the original
poster can try a different weighting scheme?


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