[phenixbb] anomalous difference map

Nathaniel Echols nechols at lbl.gov
Mon Sep 8 10:14:55 PDT 2014

On Mon, Sep 8, 2014 at 9:58 AM, CPMAS Chen <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.  An "anomalous residual map", or the
log-likelihood gradient map used by Phaser (and also available from
phenix.refine/phenix.maps), uses DANOobs - DANOcalc.  For these, what
really matters is whether you've refined anomalous scattering for the
atom(s) in question.  I've uploaded some slides showing practical examples:


Regarding Phil's comment, it probably isn't having much of an effect on
phases (and certainly very little risk of bias), but it will have a
significant impact on amplitudes and resulting peak heights.

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