Re: [phenixbb] anomalous difference map

Hi, All Please correct me if I am wrong on this. Suppose I have a peak in the anomalous difference map, I should place Br (in my case) at the peak position, while the other part of the molecule in the peak of the difference map. Should I always expect to see the overlaps of these two peaks? at some positions, I see they are apart by 1~2A. Thanks! Charles On Wed, Sep 10, 2014 at 9:10 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 wrote:

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On Tue, Sep 9, 2014 at 8:40 AM, CPMAS Chen wrote:

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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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-- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************