Re: [phenixbb] anomalous difference map

Hi Scott, three relevant papers that I'm aware of: Acta Cryst. (2012). D68, 454-467 Statistical quality indicators for electron-density maps I. J. Tickle Lang PT, Holton JM, Fraser JS, Alber T. Protein structural ensembles are revealed by redefining x-ray eletron density noise. PNAS USA. 111 237-247 Acta Cryst. (2014). D70, 2593-2606 Metrics for comparison of crystallographic maps A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams Pavel On 10/10/14 8:24 AM, Scott Horowitz wrote:

So I have a followup question to this comment in the thread: what is the origin of this rule of thumb of 1 and 3 sigma that people quote for non-difference and difference maps that you can find all over the internet at various sites, but nobody references? I can't find any papers on it specifically, but it's quite possible I'm not digging far enough back in time. Can anyone give me a lead?

Thanks, Scott

On Wed, Sep 10, 2014 at 9:26 AM, Pavel Afonine wrote:

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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 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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