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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: Edwin Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU Date: 2008-01-18 First: Rmerge doesn't matter. Don't even look into that column in scalepack output, you will be upset over nothing. If you collect twice as much data (360 sweep instead of 180) from the same crystal, your Rmerge will go up due to higher redundancy, but the dataset will actually get better because you measuring every reflection twice more and your I/sigma will increase by ~40%. Second: Rmerge is very important, because if it is, say, 100% (oh, those zeros in the scalepack output) it means that symmetry-related reflections vary by about 100%, so your data is a pile of garbage (at least in that resolution shell). Cut your data at the resolution where Rmerge is 30% and you will be rewarded by really low Rfactors for your final model. Plus, if you keep all the data to where I/sigma~1, your Rmerge is guaranteed to be 0.00 in the output, and what are you going to tell reviewers of your paper? Of course, truth is somewhere in the middle. If I collect on two crystals of the same type (assuming everything else is the same, such as redundancy), and one has much higher Rmerge, then I should probably choose the other one. If you cut resolution at I/sigma~1, and your overall Rmerge is about 10%, I think it's normal. But if it's 30%, you may have some unusually high level of noise in your data (satellite crystal? twinning? evil xray fairy messing with you?). So Rmerge does tell you something, but only in context with all the other information. After all, the only thing that matters is if your electron density map is interpretable. I dare to say that the quality of the map you get does correlate with Rmerge, but would I discard a dataset just because Rmerge is high without trying to solve the structure and take a look at the density? Never. Cheers, Ed. 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 -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse / CCP4bb navigationCCP4bb <-- 2008 <-- January 2008 <-- 18 January 2008 |
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