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://voices.uchicago.edu/phoebericelab/ On 2/28/20, 6:56 AM, "CCP4 bulletin board on behalf of Malý Martin" <[email protected] on behalf of [email protected]> 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://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ . 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 <[email protected]> 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 http://stef.ijs.si/ >> Head of Centre for Protein and Structure Production >> Centre of excellence for Integrated Approaches in Chemistry and >> Biology of Proteins, Scientific Director >> http://www.cipkebip.org/ >> e-mail: [email protected] >> phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biology >> fax: +386 1 477 3984 Jozef Stefan Institute >> Jamova 39, 1 000 Ljubljana,Slovenia >> Skype: dusan.turk (voice over internet: www.skype.com >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology CAS. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
