I fully agree with this! Best, Herman
-----Ursprüngliche Nachricht----- Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Phoebe A. Rice Gesendet: Freitag, 28. Februar 2020 17:03 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] What resolution - X-ray diffraction round this time EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Can we get some momentum for the "standard table 1" including TWO numbers - outer limit used in refinement, and nominal resolution based on some standard such as I/sigI =2 (or 3, or whatever the community can agree on)? That would hopefully cut down on all the reviewer complaints of overstated resolution. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://urldefense.proofpoint.com/v2/url?u=https-3A__voices.uchicago.edu_phoebericelab_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=CXNbP2DMixZriXPv1R2bTMMTnMPdy4mwce_8MJuNxlA&e= On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" <CCP4BB@JISCMAIL.AC.UK on behalf of martin.m...@ibt.cas.cz> wrote: Dear colleagues, I agree with all the previous responses, it is a pity to throw away useful high-resolution data. The problem of high-resolution cutoff estimation is also nicely summarized in another paper by Andrew Karplus and Kay Diederichs "Assessing and maximizing data quality in macromolecular crystallography" https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_pmc_articles_PMC4684713_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=lrf35lEnkEOs6pHot-cjxf9f3SI4dmCvkcL4098veOQ&e= . It is suggested using CC1/2 for the selection of the cutoff for data processing (not I/sigI or R_whatever). Later on, the decision should be validated performing the paired refinement protocol. Good luck with the argumentation. Martin On 2/28/20 11:08 AM, LMB wrote: > Ask the referee - (apart from the other suggestions here) > > ‘How would removing data Improve my model?” > > Sent from my iPad > >> On 28 Feb 2020, at 08:22, dusan turk <dusan.t...@ijs.si> wrote: >> >> Hi, >> >> Browsing through the recent discussion on EM data resolution cutoff >> it occurred to me that the X-ray diffraction community isn’t that >> unanimous either. >> >> My stand: >> >> When the default resolution cutoff provided with the data processing >> software in electron density map calculation and refinement delivers >> quality maps noisier than expected and/or too high R-factors I start >> adjusting the resolution cutoff by lowering the resolution and trying >> alternative space group. Hence, I allow the data processing programs >> to suggest where to draw the line (be it CC1/2, I/sigI, R merge, R >> sym, R p.i.m. and R r.i.m, …) , unless there are problems. >> >> Doing so, I came into a dispute with a referee who shaped his request: >> >> "It is well accepted that the criteria for resolution cutoff should >> consider both I/SigI and Rmerge for the outer most shell. For data >> sets collected at synchrotron sources, the criteria of I/SigI > 5 and >> Rmerge <50% can be taken as a good practical reference.” >> >> So where do we stand? Which are the most objective criteria for >> resolution cutoff to be used in diffraction data processing? Which >> number of shells to use when calculating the statistics? Do we have a >> consensus? >> >> best wishes, >> >> dusan turk >> >> >> >> Dr. Dusan Turk, Prof. >> Head of Structural Biology Group https://urldefense.proofpoint.com/v2/url?u=http-3A__stef.ijs.si_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=_3e4jARMhVBSasLY6-m9dOnl_vTRnBGwLgzq_9Dv6c8&e= >> Head of Centre for Protein and Structure Production >> Centre of excellence for Integrated Approaches in Chemistry and >> Biology of Proteins, Scientific Director >> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cipkebip.org_&d=DwIGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=lVmKxr1h6ivkmcYp1sQ_nzmWIfbFS5XWaQMHhaxbeeM&s=78xv1Oze-kc7Gv9avvfnElFBluCHaasC65gzTDktaDM&e= >> e-mail: dusan.t...@ijs.si >> phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. 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