[phenixbb] Target weight optimization (wxu_scale and wxu)

Pavel Afonine pafonine at lbl.gov
Mon Mar 28 14:33:50 PDT 2011

  Hi Yu,

> What is the real meaning of the 'wxu_scale' and 'wu'?
> (scale factor for X-ray/ADP_weight: wxu_scale
> ADP weight scale: wu)

see formula

Etotal = wxc_scale * wxc * Exray + wc * Egeom

in "Refinement of coordinates" chapter of phenix.refine manual:


Same for refinement of ADPs.

> During ADP refinement, it is suggested to refine the 'wxu_scale', what 
> if I change the value of 'wu'?

It is not suggested to do at all (I mean you can do it of course but 
it's not something that we recommend doing routinely). The default 
should be just fine. However at the end of refinement you may want to 
tune up the weights to get the best refinement statistics (in terms of 
R-factors), and in that case you use "optimize_wxc=true" and/or 
"optimize_wxu=true". Only in some weird cases when none of the above 
works well, you may want to try playing with wxc_scale and wxu_scale 
(out of desperation, I would say).

Please let me know if it's still not clear.


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