A difference map is used to identify whether there is anything not-modeled, say some ligands, ions. Then when I generate anomalous difference map, I should not put the ligand(which contains Br) in the model, right? Or in phenix, after I put the Br-ligand in the model, I should not see the anomalous difference density at the site, right?

Could anyone give me a confirmation of this? 

Thanks!

Charles
--

***************************************************

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

******************************************************