Correct me if I'm wrong, but the first papers to stop reporting R-anything were XFEL ones so I assumed it was a particularly bad estimator of data quality for those expt's ;-
With a more normal expt, again correct this if it's wrong, the problems with R-merge only throw it off by a few percent? Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 10 Jun 2021, 14:07, Frank von Delft wrote: > Or just boycott the journal...?? > > On 10/06/2021 14:02, Tim Gruene wrote: >> Hi Graeme, >> >> could you explain why Rmeas does not serve the same purpose as Rmerge? >> I guess Manfred (and others) have no objection to reporting Rmeas just >> instead of Rmerge. >> >> @ Christy: If one of my manuscript were rejected solely because Rmerge >> was not mentioned, I would make a phone call to the boss if the editor. >> Afterall, Rmerge can be recovered from the unmerged data, which ideally >> you did deposit at the PDB. >> >> Best, >> Tim >> >> >> On Thu, 10 Jun 2021 12:42:10 +0000 "Winter, Graeme (DLSLtd,RAL,LSCI)" >> <graeme.win...@diamond.ac.uk> wrote: >> >>> Once again I find myself jumping to the defence of this rather poor >>> statistic! >>> >>> Yes, Rmerge is a very poor estimator of "data quality" and has many >>> well published flaws related to multiplicity, but the low resolution >>> Rmerge, if combined with a multiplicity > (say) 5, is a good >>> indicator of whether the data set is "good" or there is something odd >>> going on. >>> >>> For example, if you claim a 1.6A structure with an inner shell Rmerge >>> of 0.11, 5-fold multiplicity and an overall I/sig(I) of 68 I would >>> "smell a rat" >>> >>> To me it does have a value, as an unbiased estimator of your true >>> unmerged I/sigma as it does not depend on any manipulation you have >>> done to your sigmas. It is not a good estimator of where the >>> resolution should be cut or any other decisions. >>> >>> The above situation could be an indicator that there was radiation >>> damage, for example >>> >>> There are better ways of measuring damage - Rd, Rcp, ... but these >>> are not commonplace graphs as I understand it. This little number in >>> the middle of the table does give you that hint. >>> >>> So while I would say rejecting a paper because it was not included >>> was very heavy handed, I would not like to see it erased from all >>> papers either. >>> >>> All the best Graeme >>> ________________________________ >>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of >>> Manfred S. Weiss <manfred.we...@helmholtz-berlin.de> Sent: 10 June >>> 2021 13:30 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>> Subject: Re: [ccp4bb] Should Rmerge be reported? >>> >>> Dear Cristy, >>> >>> this is really hilarious. And it just shows how attached >>> some ppl are to outdated numbers. Against better >>> knowledge. >>> >>> It has been shown many times that Rmerge is flawed >>> at various levels. >>> >>> The only reason I can see to report it is to be backwards >>> compatible. But of course, this is a really weak reason. >>> >>> I would love to see it disappear. >>> >>> All the best >>> Manfred >>> >>> Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato: >>> Dear Colleagues >>> Hope to find you all well and healthy. >>> >>> I have a question regarding Rmerge. In recent years, we have >>> published our crystallographic structures in highly respected >>> journals using CC1/2, I/sigma(I), completeness and multiplicity as >>> quality parameters for our diffraction data. >>> >>> Recently this year, We submitted a paper using the same strategy, but >>> one of the reviewers asked us to provide the Rmerge, arguing that >>> providing this data was compulsory and it was important to estimate >>> radiation damage. >>> >>> We replied to the editor arguing that Rmerge should not be used as a >>> quality parameter, as suggested by more recent literature, such as >>> the article published by Karplus and Diederichs >>> (10.1016/j.sbi.2015.07.003). We also argued that there are modern and >>> efficient methods to estimate radiation damage ( >>> doi.org/10.1107/S1600576718005241<http://doi.org/10.1107/S1600576718005241>; >>> doi.org/10.1107/S0907444909040177<http://doi.org/10.1107/S0907444909040177>). >>> It is my opinion that an experienced crystallographer can even >>> monitor radiation damage over the course of data processing. >>> >>> And our paper was rejected !!!!!!!!!!!!!!!! due to the fact I did not >>> provide Rmerge which I certainly could have done If I found necessary. >>> >>> Journals like Nature ((https://www.nature.com › documents › >>> nr-tables-xray<https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&ved=2ahUKEwiigtb19uHwAhWS3YUKHSB1AdkQFjABegQIAxAD&url=https%3A%2F%2Fwww.nature.com%2Fdocuments%2Fnr-tables-xray.doc&usg=AOvVaw1RbfYvNeiEM07FBEOohMig>) >>> and even IUCr Journals >>> (https://journals.iucr.org/f/services/structuralcommunications/) >>> still list Rmerge as a data to be reported. I always took this as a >>> suggestion since there are people still using Rmerge for data cutoff, >>> but I never took this as if Rmerge was a compulsory data to be >>> reported. >>> >>> I would like to hear the opinion of this community. Should we >>> compulsorily report Rmerge? If so, Why? >>> >>> Cheers, >>> >>> Cristy >>> -- >>> Cristina Nonato >>> Associate Professor >>> Laboratório de Cristalografia de Proteínas >>> Faculdade de Ciências Farmacêuticas de Ribeirão Preto >>> University of São Paulo >>> >>> >>> >>> ________________________________ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >>> >>> -- >>> Dr. Manfred S. Weiss >>> Macromolecular Crystallography >>> Helmholtz-Zentrum Berlin >>> Albert-Einstein-Str. 15 >>> D-12489 Berlin >>> Germany >>> >>> ________________________________ >>> >>> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH >>> >>> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher >>> Forschungszentren e.V. >>> >>> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. >>> Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech >>> (Sprecher), Prof. Dr. Jan Lüning, Thomas Frederking >>> >>> Sitz Berlin, AG Charlottenburg, 89 HRB 5583 >>> >>> Postadresse: >>> Hahn-Meitner-Platz 1 >>> 14109 Berlin >>> Deutschland >>> >>> ________________________________ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> >> >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
