[phenixbb] How to reduce clashscore value

Pavel Afonine pafonine at lbl.gov
Fri Nov 18 13:15:46 PST 2011


> 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:


see article "Improved target weight optimization in phenix.refine".

Adding H may help further.

> 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.


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