Hi Subhani,
I am refining a protein with metal-ligand complexes. Is it possible to refine only y coordinates for an atom (on two fold) while keeping X and Z fixed using Phenix?
it's taken care of automatically by phenix.refine if atom in question is close enough to the special position in the starting model. If I recall it right, "close enough" means at least 0.5A or so.
Also is there a way to calculate something like anomalous difference-difference map (Anomalous Fobs - Anomalous Fcalc) to identify any additional atoms bound at metal sites.
If you refine against anomalous data set (containing Fobs+ and Fobs-) then traditional anomalous difference map will be output by phenix.refine by default. Recent versions should have the ability to create LLG maps as well. Pavel