[phenixbb] anomalous difference map

CPMAS Chen cpmasmit at gmail.com
Tue Sep 9 08:40:06 PDT 2014

Hi, All

Is it possible that I have anomalous and LLG peak, but I have no difference
density peak? In this case, is that because the model I have is not good
enough or the diffraction data at this site of the model is missing?



On Mon, Sep 8, 2014 at 1:23 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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.
> 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



Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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