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. Pavel.