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 <[email protected]> wrote:
On Tue, Sep 9, 2014 at 8:40 AM, CPMAS Chen <[email protected]> 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 



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Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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