On Tue, Nov 20, 2012 at 12:59 PM, Pavel Afonine
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.
Which is *not* the same thing - the anomalous difference map Phenix outputs only shows the anomalous differences in F-obs, and not the difference between F-obs and F-calc. As a result, any weaker anomalous scatterers (like chlorine, etc.) may have their signal drowned out by the contribution of the metals. -Nat