[phenixbb] anomalous difference map

[Pavel Afonine]

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 <pafonine at lbl.gov> wrote:
>> 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> wrote:
>>> On Tue, Sep 9, 2014 at 8:40 AM, CPMAS Chen <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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>
>