[phenixbb] coordinate refinement and maps

Pavel Afonine pafonine at lbl.gov
Tue Nov 20 12:59:55 PST 2012

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.


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