[phenixbb] wxu scale in phenix.refine

Jan Abendroth jan.abendroth at gmail.com
Tue Sep 18 09:35:26 PDT 2007

Hi Pavel,
thanks a lot for your fast response!
Here some clarification:
- somehow, the adjustments of the B weights were not taken into account at
all. Ie. a "diff" on the pdb-files from jobs run with wxu_scale=0.5 and
wxu_scale=2.0 shows that they are identical. While the log file acknowledges
the "Command line parameter definitions" for wxu_scale=1 and wxc_scale=2,
during the refinement section it states that wxc_scale = 1.0 and wxu_scale=
- yes, I included a TLS refinement. Are TLS refinement ans wxu_scale
mutually exclusive? How would one proceed in this situation?


On 9/18/07, Pavel Afonine <pafonine at lbl.gov> wrote:
> 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.
> Pavel.
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