Dear Manfred, I completely agree. However this is not routinely reported.
The discussion is of removing one indicator of this signal, rather than replacing it with a superior measure - the latter is something I would more actively support however would involve adding new stuff which is an uphill battle. All the best Graeme ________________________________ From: Manfred S. Weiss <manfred.we...@helmholtz-berlin.de> Sent: 10 June 2021 13:43 To: Winter, Graeme (DLSLtd,RAL,LSCI) <graeme.win...@diamond.ac.uk>; CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Should Rmerge be reported? Dear Graeme, a better number to look at is Isa. Instead of low resolution Rmerge. Seriously. We monitor that to assess beamline performance. Cheers, Manfred Am 10.06.2021 um 14:42 schrieb Winter, Graeme (DLSLtd,RAL,LSCI): 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><mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Manfred S. Weiss <manfred.we...@helmholtz-berlin.de><mailto:manfred.we...@helmholtz-berlin.de> Sent: 10 June 2021 13:30 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK><mailto: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 -- 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. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom -- 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 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/
