[phenixbb] anomalous difference map

Pavel Afonine pafonine at lbl.gov
Mon Sep 8 10:23:19 PDT 2014

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


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