That is extremely likely! - certainly REFMAC will do that.. If 5% missing using DFcalc is a good thing - if 35% is missing not wise.. Eleanor
On Mon, 4 Mar 2024 at 07:53, Ben Bax <ben.d.v....@gmail.com> wrote: > > Fcalc maps look fantastic. Are you sure they were not using an Fcalc for > the missing 35% of the data? > Ben > > > On 29 Feb 2024, at 21:33, Rafael Marques <rafael_mmsi...@hotmail.com> > wrote: > > Sorry for jumping into the post, but I would like the community’s opinion > about completeness, once this topic was raised here. What could be > considered reasonable? Recently I have seen a 65% completeness Crystal > structure and, surprisingly, the electron density map was not that bad for > a > 3.2 A structure. How such a nice map could have been calculated with > such poor parameters? I could only think of anisotropy. > > Best > > > Rafael Marques da Silva > PhD Student – Structural Biology > University of Leicester > > Mestre em Física Biomolecular > Universidade de São Paulo > > Bacharel em Ciências Biológicas > Universidade Federal de São Carlos > > phone: +55 16 99766-0021 > > * "A sorte acompanha uma mente bem treinada"* > *________________________________________________* > > ------------------------------ > *De:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> em nome de Paul Adams < > pdad...@lbl.gov> > *Enviado:* Wednesday, February 28, 2024 2:58:16 PM > *Para:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Assunto:* Re: [ccp4bb] Rwork and Rfree the same? > > > 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 > > 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> 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 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > 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 > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > 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 > ######################################################################## 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/
