[phenixbb] R, Rfree, and wxu_scale

Pavel Afonine pafonine at lbl.gov
Sun Aug 5 08:38:52 PDT 2007

Hi Jianghai,

> In the manual, I have also seen examples to manually set the target 
> weight (target_weights.fix_wxc and target_weights.fix_wxu).  But there 
> is no explanations for their uses.  What kind of effects would they cause?

These parameters are used to fix the weights to user specified values. 
In this case the weights are not determined automatically anymore, but 
the program uses whatever is given by target_weights.fix_wxc and 
target_weights.fix_wxu (one exception could be for TLS+ADP, but I do not 
remember exactly).

If target_weights.fix_wxc and target_weights.fix_wxu are used, then the 
total targets are:

refinement of coordinates: Etotal = fix_wxc * Exray + wc * Egeom
refinement of ADP: Etotal = fix_wxu * Exray + wu * Eadp

Note, by default the targets are:

refinement of coordinates: Etotal = wxc * wxc_scale * Exray + wc * Egeom
refinement of ADP: Etotal = wxu * wxu_scale * Exray + wu * Eadp

where wxc and wxu are determined automatically (similar to CNS); 
wxc_scale and wxu_scale are the scales to provide a room for manual 
adjustment of this values (if really necessary).

Once again (for your information), all these will be explained in 
phenix.refine documentation in the next upcoming release.


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