[phenixbb] anomalous difference map

CPMAS Chen cpmasmit at gmail.com
Mon Sep 8 11:08:20 PDT 2014

Thanks, all. It did clear my thought. Because I always wondering why the
LLG map is getting more different from the anomalous difference map and
getting close to the 2FoFc map, while the anomalous difference map is
almost the same as the beginning when I have no ligand put in the model.


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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140908/60384bd7/attachment.htm>

More information about the phenixbb mailing list