[phenixbb] wxu scale in phenix.refine

Pavel Afonine pafonine at lbl.gov
Tue Sep 18 08:35:34 PDT 2007

Hi Jan,

> in the final stages of refining a structure, I would like to optimize 
> the restraint weights for geometry and B factors.

Good idea! Although phenix.refine computes "optimal" weight 
automatically, the values vary from structure to structure.

> It seems to work fine for geometry by defining 
> "refinement.target_weights.wxc_scale=1.0".

Yes, I would try an array of values 0.25, 0.5, 1.0, 1.5, 2.0, 2.5.

> However, when the respective definition for B-factors does not seem to 
> have an impact at all.

This is very weird. We exercise this in out tests regularly, so it 
changing wxu_scale should have an impact. It may be that values range 
for you structure is somehow different... Can you try the extreme 
values: very big (wxu_scale=10) and very small (wxu_scale=0.1) and see 
if this makes a difference? Are you using TLS (if yes, then this 
behavior is explainable)?
> The main reason why I try to fiddle around with the B-weights is that 
> coot gives me a whole bunch of red bars in the Temperature factor 
> variance analysis...

The variability of ADP depends on many factors: resolution, model  used 
for global motion (TLS), how internal degrees of freedom modeled ... I 
do not know if Coot analysis takes this all into account. Otherwise I 
would use the "red bars" analysis with some care.


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