Tim, can I explain? To be honest no! Other than old habits and all. Should converge to the same value in the end, so you have a valid point.
All the best Graeme ________________________________ From: Tim Gruene Sent: Thursday, June 10, 2021 14:02 To: Winter, Graeme (DLSLtd,RAL,LSCI) Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Should Rmerge be reported? 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 > -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. 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