[phenixbb] coordinate refinement and maps

[Nathaniel Echols]

On Tue, Nov 20, 2012 at 12:59 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
>> 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