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Re: [ccp4bb] differences between Rsym and Rmerge |
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CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008Subject: Re: differences between Rsym and Rmerge From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK Date: 2008-01-18 reciprocal cell axes. Dead handy... price@UCHICAGO.EDU wrote: > 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 >>> 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 > > --------------------------------------------------------------------------------------------------------------------------- > > 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 CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008 |
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