[phenixbb] optimize_wxc and wxu

[Pavel Afonine]

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 <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
>     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.
>
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
> -- 
> 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>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090408/6579608d/attachment-0003.htm>