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Re: [ccp4bb] sigma cutoff for fitting waters in model
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Fwd: Re: SUMMARY: scala and xds data
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-04-26		Next message:
Subject: Re: Rsym problems...maybe???
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-26


Subject: Re: sigma cutoff for fitting waters in model
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-26

I am a bit out of touch with the discussion, and this may have been
mentioned already.
It is important to remember that Sigma is an OVERALL value for the whole
map, whereas one is looking for local solutions when fitting any
density. Stuff on the surface of the molecule ought to be contoured at a
lower level than in the ore, and this applies to protein as well as waters.

Eleanor


Ed Pozharski wrote:
> On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote:
>> The "0.3% chance" of a peak being above 3
>> "sigmas" assumes that the histogram of electron density values is
>> Gaussian. It is not! In fact, it is a funny-looking bimodal
>> distribution (the peaks are protein and solvent regions).
>
> Indeed! That's why it is a "bizarre" argument. In fact, standard
> deviation is rather meaningless unless one is dealing with "univariate"
> distribution. For bimodal distributions, changes of standard deviation
> are uninterpretable (without looking at the distribution, that is) since
> they can be due to both shifts and redistribution.
>
> Cheers,
>
> Ed.
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Fwd: Re: SUMMARY: scala and xds data
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2010-04-26		Next message:
Subject: Re: Rsym problems...maybe???
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-04-26
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