[phenixbb] coordinate refinement and maps
pafonine at lbl.gov
Tue Nov 20 12:59:55 PST 2012
> 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.
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