[phenixbb] anomalous difference map

[Scott Horowitz]

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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-- 
Scott Horowitz, Ph.D.
Research Associate
Howard Hughes Medical Institute

University of Michigan
Department of Molecular, Cellular, and Developmental Biology
Bardwell lab
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phone: 734-647-6683
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