You know there is that other funny column with chi^2's. I like to quote both. Half of the reviewers will know which column to look at, but you will satisfy the other half.
Bernie On Fri, January 18, 2008 1:39 pm, Edwin Pozharski wrote: > There are two opposing views on this. > > 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 >>> [EMAIL PROTECTED] >>> **************************************************** >>> >>> >>> -----Original Message----- >>> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] 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 / >
