- 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=2.16.

On 9/18/07, Pavel Afonine <pafonine@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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