[phenixbb] anomalous difference map

[Pavel Afonine]

Hi Charles,

I think the key here is what you call "no difference density peak". 
Sites may be partially occupied so rule of thumb for choosing contouring 
levels for 2mFo-DFc and mFo-DFc maps (1 and 3 sigma, correspondingly) 
may not be appropriate, for instance.

Pavel

On 9/10/14 6:10 AM, CPMAS Chen wrote:
> Thanks, Nat.
>
> If this is noise, why the anomalous or LLG peaks could be as high as 5 
> ~ 6 sigma?
>
> Charles
>
> On Tue, Sep 9, 2014 at 5:58 PM, Nathaniel Echols <nechols at lbl.gov 
> <mailto:nechols at lbl.gov>> wrote:
>
>     On Tue, Sep 9, 2014 at 8:40 AM, CPMAS Chen <cpmasmit at gmail.com
>     <mailto:cpmasmit at gmail.com>> wrote:
>
>         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?
>
>
>     You should at a minimum see > 1sigma density in the 2mFo-DFc map,
>     and if the site is unmodeled (or modeled as a water) you should
>     see an mFo-DFc peak as well.  If neither of these applies, the
>     anomalous and LLG peaks are probably just noise.
>
>     -Nat
>
>
>
>
> -- 
>
> ***************************************************
>
> Charles Chen
>
> Research Associate
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>

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