[phenixbb] wxu scale in phenix.refine
pafonine at lbl.gov
Tue Sep 18 09:45:57 PDT 2007
Yes, I'm copying the response for exactly the same question that I wrote
a week ago or so...
Playing with wxu_scale is how you change the strength of ADP restraints
in all cases except when you do combined "TLS+individual ADP"
refinement. In order to make the TLS refinement very robust and
efficient we re-refined ~350 TLS containing structures from PDB
performing the grid search for wxu_scale parameter and we found some
"optimal" values for wxu_scale as a function of resolution. We use these
values in automatic adjustment that you are mentioning. So currently
there is no way you can turn off this adjustment; however I realize that
users may want to play with wxu_scale themselves and skip the
adjustments so I will provide this option in future.
As a possible solution to keep going now you can try this two-step
step 1: Refine your model with default strategy
(strategy=individual_sites+individual_adp) making sure that the ADP
restraints are tight enough (play with wxu_scale) to produce the
B-factors distribution that you like.
step 2: Refine the best model out of "step 1" with the
strategy=individual_sites+group_adp+tls. This will preserve the
distribution of B-factors in the model from "step 1" and will add TLS
model on top of it.
Please let me know if you have any questions/problems!
Jan Abendroth wrote:
> 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=2.16.
> - 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
> <mailto:pafonine at lbl.gov>> wrote:
> Hi Jan,
> > in the final stages of refining a structure, I would like to
> > 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
> > 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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