[phenixbb] anomalous difference map

Dale Tronrud detBB at daletronrud.com
Mon Sep 22 10:18:30 PDT 2014

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On 9/19/2014 10:05 AM, CPMAS Chen wrote:
> Hi, Phil,
> Is it right to model the whole ligand molecule to the anomalous 
> difference map? For some sites, the overlap between anomalous
> difference and difference map is small, while the anomalous
> difference or difference map itself is rather big.  The anomalous
> difference is way bigger than a single Br can be.

   The anomalous map will only show the density of anomalously
scattering electrons, which won't even be the entire bromine atom.  If
the rest of you ligand is composed of carbon, oxygen, and nitrogen
atoms they will be invisible in the anomalous map.  If the anomalous
density is "bigger" than a bromine atom, either the resolution of your
map is low (remember the anomalous signal likely does not go to as
high a resolution as your normal signal) or the bromine atom is
disordered a bit.

Dale Tronrud

> Thanks!
> Charles
> On Mon, Sep 8, 2014 at 1:10 PM, Phil Jeffrey
> <pjeffrey at princeton.edu <mailto:pjeffrey at princeton.edu>> wrote:
> In your first sentence your meaning of "difference map" is: ( F_obs
> - F_calc ), phases
> For an anomalous difference map you're calculating: ( F(+) - F(-)
> ), phases-90
> So you would still expect to see a peak in the anomalous
> difference map in the presence of the anomalous scatterer since you
> are not subtracting off its contribution to the scattering.
> There probably would be (very) small differences in the phases 
> dependent on whether you explicitly model the Br as an anomalous 
> scatterer or not but I have never experimented to see if that
> makes a small impact on an anomalous difference map.
> Cheers, Phil Jeffrey Princeton
> --
> ***************************************************
> Charles Chen
> Research Associate
> University of Pittsburgh School of Medicine
> Department of Anesthesiology
> ******************************************************
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