High R "merges" with no reasonable excuse can certainly be a useful
red flag during data processing (along with the % of observations
rejected, which I've never had a reviewer request).
Which brings up the point that one reasonable excuse is anisotropy -
high Rs for merging random observations in the "imaginary" direction
will be combined with lower Rs for merging decent data in the "real"
direction.
Is there any extant software that will calculate directionally-binned
Rmerges? It would be useful both for re-assuring users that there
isn't anything worse with their data, and for arguing with referees
who don't read CCP4BB.
Phoebe
At 01:18 PM 1/18/2008, 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]
>
>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
>>[log in to unmask]
>>****************************************************
>>
>>
>>-----Original Message-----
>>From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>>Chris Putnam
>>Sent: Friday, January 18, 2008 1:21 PM
>>To: [log in to unmask]
>>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
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
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