[phenixbb] anomalous difference map

CPMAS Chen cpmasmit at gmail.com
Tue Sep 9 09:13:55 PDT 2014


I have a similar question about this. when the anomalous difference map
identify possible sites for Br(in my case), I should also expect to see the
difference map peak at this site. If not, could this "Br" be something else?

Thanks!

Charles

On Tue, Sep 9, 2014 at 11:40 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:

> 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?
>
> Thanks!
>
> Charles
>
> 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
>
> ******************************************************
>
>


-- 

***************************************************

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

******************************************************
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