[phenixbb] How to reduce clashscore value
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
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
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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