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Re: [ccp4bb] Sigma Cutoff in HKL2000 Data Processing
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Sigma Cutoff in HKL2000 Data Processing
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-10-22		Next message:
Subject: Re: Question about merging of data from different crystals
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-10-22


Subject: Re: Sigma Cutoff in HKL2000 Data Processing
From: "Edward A {- dot -} Berry" BerryE {- at -} UPSTATE {- dot -} EDU
Date: 2009-10-22

The default sigma cutoff (in denzo) is -3 and I wouldn't override that
without good reason. The cut-off is applied before averaging equivalent
reflections (but after adding partials?). If you reject all negative
observations of a particular reflection and average the remaining
positive observations, you will get an artificially inflated estimate
of the intensity.

Even if the intensity is negative after averaging, the French&Wilson
treatment in truncate will give you a positive F in the end.
Apparently there is some information in the negative reflections,
i.e. the most likely value of Fobs for a reflection with Iobs= -0.01 sigma
is greater than that for a reflection with Iobs=-1.5 sigma.
Ed

protein.chemist protein.chemist wrote:
> What is the Sigma Cutoff that one should use for Data Processing using
> HKL2000.
>
> Is there a minimum or maximum value.
>
> Also if there is a variation then what all does it depend on.
>
> Thanks in Advance for your help.
>
> Mariah
>
> --
> Mariah Jones
> Department of Biochemistry
> University of Florida

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Sigma Cutoff in HKL2000 Data Processing
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-10-22		Next message:
Subject: Re: Question about merging of data from different crystals
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-10-22
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