[phenixbb] optimize_wxc and wxu

Morten Grøftehauge morteng at bioxray.au.dk
Wed Apr 8 04:36:49 PDT 2009

Just a quick question/comment,

I may remember this incorrectly but isn't the best wxu_scale=1.81 when you
use TLS? Older versions of phenix.refine changed it automatically when you
applied TLS IIRC but now it only goes to 1.81 if I use the optimize_wxu
Am I remembering correctly or is my headache screwing with me?


2009/1/26 Pavel Afonine <pafonine at lbl.gov>

> Hi Scott,
> > In general should one optimize wxc and wxu ONLY as a final polishing
> > step or can this be done earlier in the refinement and then the
> > optimized values used for subsequent rounds of refinement?
> Optimizing weights is time consuming: depending on the data and model
> size it can take from many minutes to hours, and this is the only reason
> for suggesting it as a final step.
> However if it runs quickly or/and you are not in rush, you can do it all
> the time: then it will always make sure that the weights are "optimal"
> (in terms of giving the best Rfree). Note, that most of the time you
> don't really need it since the automatically determined weights are
> pretty good (most of the time).
> The optimal weight found after running phenix.refine with
> optimize_wxc=true (or/and optimize_wxu=true) may substantially vary
> between structure determination stages or even between refinement
> macro-cycles within one refinement run. This is why it is not generally
> advised to use the same weights (determined at the beginning) all the
> time, although technically you can: just pick up the best wxc_scale from
> the log file and specify it for the next run.
> Please let me know if you have any questions!
> Pavel.
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Morten K Grøftehauge
PhD student
Department of Molecular Biology
Gustav Wieds Vej 10 C
8000 Aarhus C - Denmark
Phone: +45 89 42 52 61
Fax: +45 86 12 31 78
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