On Mon, Sep 8, 2014 at 9:58 AM, CPMAS Chen <cpmasmit@gmail.com> wrote:

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?

An "anomalous difference map" is a map of the anomalous differences DANO (Fobs(+) - Fobs(-)).  It's independent of  Fcalc, so it doesn't matter if you put the ligand in or not. 

This is not quite an accurate statement. To calculate a Fourier map one requires amplitudes and phases. (Fobs(+) - Fobs(-)) are the amplitudes for the anomalous difference map. The phases come from Fcalc (actually from Fmodel), one way or another.

Pavel