[phenixbb] anomalous difference map

CPMAS Chen cpmasmit at gmail.com
Fri Sep 19 10:05:54 PDT 2014

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.



On Mon, Sep 8, 2014 at 1:10 PM, Phil Jeffrey <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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