[phenixbb] wxu scale in phenix.refine

[Jianghai Zhu]

I will chime in.  Is it possible for phenix.refine to get the TLS
parameters from a previous run? then we can change wxu_scale value
during an individual_adp refinement in the presence of fixed TLS
parameters.

Jianghai

On Tue, 2007-09-18 at 09:45 -0700, Pavel Afonine wrote:
> Yes, I'm copying the response for exactly the same question that I wrote 
> a week ago or so...
> 
> Part 1:
> 
> 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.
> 
> Part 2:
> 
> As a possible solution to keep going now you can try this two-step 
> refinement:
> 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!
> Pavel.
> 
> 
> 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?
> >  
> > Cheers
> > Jan
> >
> >  
> > 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
> >     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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