Dear Justin, Be careful of the reported “fill-in” effect of unobserved data by some refinement programs (not sure if this is your case or even if it was, whether it may cause the Rfactor to be identical) when using anisotropic cut-off.
It is documentated here: https://staraniso.globalphasing.org/test_set_flags_about.html BW, D > On 28 Feb 2024, at 18:07, Rasmus Fogh <rhf...@globalphasing.com> wrote: > > > CAUTION: This email originated from outside of the LMB: > .-owner-ccp...@jiscmail.ac.uk-. > Do not click links or open attachments unless you recognize the sender and > know the content is safe. > If you think this is a phishing email, please forward it to > phish...@mrc-lmb.cam.ac.uk > > > > Dear All, > > In addition to Paul Adams point, I would note that people have sometimes been > confused by different definitions of completeness and resolution when looking > at Staraniso data, particularly if there is significant anisotropy. It would > be worth checking not only which shell but which definition the 38% > completeness figure refers to, and what the anisotropic diffraction limits > are. > > Yours, > Rasmus Fogh > >> On 28/02/2024 17:58, Paul Adams wrote: >> By setting wxc (weight of the X-ray term) to 0.1 there is good chance that >> the refinement is dominated by the geometry term and the model isn’t really >> seeing the effect of the X-ray data. I suspect this would result in >> R-factors that are similar. Why they are so low is less clear, but as others >> have pointed out 38% completeness is a problem. It would be good to check if >> that is 38% overall, or just very incomplete in the higher resolution >> shells. If it is complete at lower resolution you might be able to do >> something with the dataset, but not using the default parameterization in >> refinement programs - you’ll need to apply constraints and additional >> restraints if you can, and look at the weighting (by modifying wxc_scale, >> not wxc). >> There is a Phenix mailing list you might want to use as well (I assume you >> are using phenix.refine): >> https://phenix-online.org/mailman/listinfo/phenixbb >> <https://phenix-online.org/mailman/listinfo/phenixbb> >>>> On Feb 28, 2024, at 8:21 AM, Justin Cruite <jcru...@crystal.harvard.edu> >>>> wrote: >>> >>> Thanks everyone, >>> >>> I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset. >>> The data was processed using autoProc and the staranisano mtz was used for >>> MR. The completeness is only 38%. It could be that the Rfree and Rwork >>> reflection sets are small because of this? What is the best way to check >>> the number of reflections used for Rwork and Rfree? Is this dataset usable >>> at all? >>> >>> Thanks! >>> >>> Justin >>> >>>> On Wed, Feb 28, 2024 at 10:21 AM nicfoos <nicf...@embl.fr >>>> <mailto:nicf...@embl.fr>> wrote: >>> >>> Hello Justin, >>> >>> There is something weird in your results. You mention Rwork/Rfree of >>> 0.1837. >>> This means a pretty good refinement and also is very unusual to be >>> obtain for a resolution of 3.37. >>> Additionally you should not have Rfree = Rwork. >>> I suspect something wrong with you Rfree reflections sets. What >>> size is >>> it ? Is your dataset complet ? >>> How did you cut the res. ? >>> >>> I hope this may help you. >>> >>> Nicolas >>> >>> >>> >>>> On 2024-02-28 16:10, Justin Cruite wrote: >>> > Hi everyone, >>> > >>> > What does it mean if your Rwork and Rfree are exactly the same? >>> > >>> > I solved a 3.37 Å structure with Phaser-MR and immediately ran 10 >>> > cycles of refinement with wxc = 0.1. Everything else at default. The >>> > Rwork and Rfree are both 0.1837. Is this bad? >>> > >>> > Thank you! >>> > >>> > Justin >>> > >>> > ------------------------- >>> > >>> > To unsubscribe from the CCP4BB list, click the following link: >>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <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 >>> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> >>> >> -- >> Paul Adams (he/him/his) >> Associate Laboratory Director for Biosciences, LBL >> (https://biosciences.lbl.gov) >> Principal Investigator, Computational Crystallography Initiative, LBL >> (http://cci.lbl.gov) >> Vice President for Technology, the Joint BioEnergy Institute >> (http://www.jbei.org) >> Principal Investigator, ALS-ENABLE, Advanced Light Source >> (http://als-enable.lbl.gov) >> Laboratory Research Manager, ENIGMA Science Focus Area >> (http://enigma.lbl.gov) >> Adjunct Professor, Department of Bioengineering, UC Berkeley >> (http://bioeng.berkeley.edu) >> Member of the Graduate Group in Comparative Biochemistry, UC Berkeley >> (http://compbiochem.berkeley.edu) >> Building 91, Room 410 >> Building 978, Room 4126 >> Tel: 1-510-486-4225 >> http://cci.lbl.gov/paul >> ORCID: 0000-0001-9333-8219 >> Lawrence Berkeley Laboratory >> 1 Cyclotron Road >> BLDG 91R0183 >> Berkeley, CA 94720, USA. >> Executive Assistant: Michael Espinosa [ meespin...@lbl.gov ][ 1-510-333-6788 >> ] >> Phenix Consortium: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ] >> -- >> ------------------------------------------------------------------------ >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > > -- > Rasmus H Fogh Tel.: +44 (0)1223 353033 > Global Phasing Ltd., Fax : +44 (0)1223 366899 > Sheraton House, Castle Park, > Cambridge CB3 0AX, United Kingdom > > ######################################################################## > > 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/
