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Re: [ccp4bb] differences between Rsym and Rmerge
 

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CCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008
Previous message:
Subject: Re: differences between Rsym and Rmerge
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-01-18 		Next message:
Subject: How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-01-18


Subject: Re: differences between Rsym and Rmerge
From: Chris Putnam cdputnam {- at -} UCSD {- dot -} EDU
Date: 2008-01-18
On Friday 18 January 2008 11:18:45 am Mischa Machius wrote:
> OK, that brings us back to a more substantial question: is any of  
> these R values actually suitable to judge the quality of a given  
> dataset? Instead of introducing novel R factors, one could also simply  
> ignore them altogether, make sure that the error models have been  
> properly chosen and look at I/sigma(I) as the main criterion.  
> [QUOTE ]If anyone then still wants to present low R factors, one can  
> always divide by 2, if necessary. [/QUOTE]

Your point is well taken, and I don't disagree that relying
solely on Rsym/Rmerge can be a treacherous course for any
crystallographer.

But before I drop the "novel R factors" (actually we're all
apparently reporting some version of them, but we're not
being very clear), I'll interject two interesting features
that reporting all three of them together could provide:

Comparison of Rhkl vs Rrot provides some 'test' on the chosen
Laue group during processing.

Comparison of Rhkl vs Rrot vs RBijvoet (especially if each
value is reported with overall redundancies) begins to
approach some of the features captured by the proposed
Rmeas (Diederichs & Karplus, Nat. Struct. Biol. 1997 4:269)
as the number of individual measurements will increase
from Rhkl to Rrot to RBijvoet. (For crystals with significant
anomalous signal, RBijvoet clearly won't be useful for this 'test.')

I won't belabor this point (or defend this view) any further,
though I will repeat my surprise at the lack of a clear
consensus for what Rsym and Rmerge actually mean,
as opposed to things like I/sigma, for example.

Chris.


Copied and pasted as these new names for R factors only
exist in my mind:

> Rhkl - R of identical hkl's
>
> Rrot - R of symmetry-related hkls, but not Bijvoet pairs
> ("rot" coming from the concept that all symmetry-related
> reflections can be found via rotations in reciprocal space and
> the fact that "sym" has already been used)
>
> RBijvoet - R of symmetry-related and Bijvoet-related hkls
> (including reflections related by both rotations and an inversion
> center in reciprocal space)
>
> Rhkl,multi - multi-crystal version of Rhkl
>
> Rrot,multi - muti-crystal version of Rrot
>
> RBijvoet,multi - multi-crystal version of RBijvoet


--
Christopher Putnam, Ph.D.
Assistant Investigator
Ludwig Institute For Cancer Research

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008
Previous message:
Subject: Re: differences between Rsym and Rmerge
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-01-18 		Next message:
Subject: How to refine a structure with ATP and AMP and pyrophosphate sharing the same density in CCP4i?
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-01-18


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