[phenixbb] optimize_wxc and wxu
PAfonine at lbl.gov
Wed Apr 8 08:18:31 PDT 2009
- when optimize_wxu=true is used the weight may be any that gives the
best Rfree. The optimized value is used only for a given run and not
propagated to .def file.
- if "tls+individual_adp" is used (and optimize_wxu=false) then the
weight is set up automatically to a value found from systematic
re-refinement of models from PDB.
On 4/8/09 4:36 AM, Morten Grøftehauge wrote:
> 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 option.
> Am I remembering correctly or is my headache screwing with me?
> 2009/1/26 Pavel Afonine <pafonine at lbl.gov <mailto: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
> 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
> 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!
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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
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