Hi Morten, - 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. Pavel. 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?

Sincerely, Morten

2009/1/26 Pavel Afonine mailto:[email protected]>

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 www.bioxray.dk http://www.bioxray.dk

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