On Fri, Nov 18, 2011 at 1:15 PM, Pavel Afonine <pafonine@lbl.gov> wrote:
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, respectively).
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?
Regards,
Tim