Re: [ccp4bb] differences between Rsym and Rmerge

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CCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008

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Subject: Re: differences between Rsym and Rmerge
From: "Salameh, Mohd A {- dot -} , Ph {- dot -} D {- dot -} " Salameh {- dot -} Mohd {- at -} MAYO {- dot -} EDU
Date: 2008-01-18

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Subject: Re: differences between Rsym and Rmerge
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-01-18

Subject: Re: differences between Rsym and Rmerge
From: Mischa Machius Mischa {- dot -} Machius {- at -} UTSOUTHWESTERN {- dot -} EDU
Date: 2008-01-18

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]

Best - MM

On Jan 18, 2008, at 1:02 PM, Salameh, Mohd A., Ph.D. wrote:

> Thank you all, it was very, very helpful discussion. However, I
> collected crystal data and the Rmerge overall was very high around
> 0.17
> at 2.6A resolution and I'm wondering what is the acceptable value
> (range) of R-merge that worth the time to continue processing! Very
> anxious to hear your thoughts. Thanks, M
> ****************************************************
> Mohammed A. Salameh, Ph.D.
> Mayo Clinic Cancer Center
> Griffin Cancer Research Building
> 4500 San Pablo Road
> Jacksonville, FL 32224
> Tel:(904) 953-0046
> Fax:(904) 953-0277
> salameh.mohd@mayo.edu
> ****************************************************
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Chris Putnam
> Sent: Friday, January 18, 2008 1:21 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] differences between Rsym and Rmerge
>
> On Friday 18 January 2008 09:30:06 am Ethan A Merritt wrote:
>>
>> Rmerge is an average over replicate measurements of the intensity for
>> identical [hkl]. Rsym is an average over the measurements for all
> symmetry
>> equivalent reflections.
>>
>> In the presence of anomalous scattering, Rsym will be higher than
> Rmerge
>> because the Bijvoet pairs, although symmetry related, do not have
> identical
>> intensities.
>>
>> One might logically report two values for Rsym, one which averages
>> over the Bijvoet-paired reflections and one which does not.
>>
>
> This has been an eye-opening discussion for me. I've been really
> surprised
> that there's been such a diversity of opinion about what these common
> terms ought to refer to, and the fact that my understanding was wrong.
> I always thought that Rsym was an average over all symmetry equivalent
> reflections from the same crystal (including Bijvoet pairs) and Rmerge
> was
> properly restricted to cases of multi-crystal averaging. (My versions
> of
> Table 1's from single crystals have used "Rsym" rather than "Rmerge".)
>
> I wonder if the problem here is that the terms have become overloaded
> (and
> hence non-specific). In that sense "Rmerge" is a particularly
> unfortunate
> name as every R that we're discussing is a really a merge of some sort
> or
> another. (In the most naive sense, "Rmerge" might be thought to be
> the
> R
> for whatever variation of reflection merging the experimenter
> chooses to
> do.)
>
> One possible solution would be to push the community towards a new set
> of
> terms with clearly defined meanings (and whose names would be used
> explicitly by new releases of MOSFLM, HKL2000, etc. and changes for
> new entries in the PDB).
>
> If new terms were to be adopted, they ought to specifically
> distinguish
> between single crystal and multi-crystal merging. I see three such
> R values that might be useful (I've arbitrarily chosen names to
> distinguish
> them from each other and the older terms):
>
> 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
>
> The downside of adopting new names is that it makes the previous
> literature
> obsolete, but I wonder if the older terms were ambiguous enough that
> that's
> not such a problem.
>
>
> --
> Christopher Putnam, Ph.D.
> Assistant Investigator
> Ludwig Institute For Cancer Research

--------------------------------------------------------------------------------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353

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Next message:
Subject: Re: differences between Rsym and Rmerge
From: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-01-18