Think of completeness with an analogy to turkey. Say you happen to find a one-legged turkey (incomplete by conventional standard) you could still stuff it and put it in the oven and enjoy 93% of the turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)
Happy Thanksgiving everyone Jürgen P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & Kartoffelknödel > On Nov 28, 2019, at 4:38 PM, Bernhard Rupp <hofkristall...@gmail.com> wrote: > > Sorry for being late on this thread - > > but the completeness myth is one of these conventional wisdoms I am seriously > questioning and completeness > as a global statistic is almost uninformative, short of telling you 'fewer > than all recordable reflections up to the reported > (likely isotropic) resolution limit given whatever (likely isotropic) cutoff > was applied'. Sounds not very clear to me. > > Kay mentioned already that any information is better than no information, > with the caveat that you cannot expect > map quality (being an upper limit for model quality - not going into > precision vs accuracy issue here) corresponding to > the highest resolution reported, which is in reality frequently anisotropic > (but not reported or reflected adequately > in the PDB reports). > We posted some remarks to this effect recently, pointing out that highly > incomplete and anisotropic data can still > yield limited but useful information as long as your claim remains > correspondingly modest. Section 3.4 in > http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html > > Having said that, while random incompleteness is not problematic, systematic > reciprocal space incompleteness leads > to corresponding systematic real space effects on the map, the simplest being > anisotropic data reflecting anisotropic > reciprocal map resolution. This is different for example when wedges are > missing or absence of serial extinctions makes > space group determination more challenging (although we are almost in the age > where 'record 360 deg of data and > try every SG' works). James Holton has video examples for incompleteness > effects and some images are also in my book. > https://bl831.als.lbl.gov/~jamesh/movies/ > > Cheers & Happy Thanksgiving, BR > > PS: A systemic rant regarding data quality representation can be found here > https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2 > > ------------------------------------------------------ > Bernhard Rupp > http://www.hofkristallamt.org/ > b...@hofkristallamt.org > ------------------------------------------------------ > All models are wrong > but some are useful. > ------------------------------------------------------ > > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Kay Diederichs > Sent: Monday, November 25, 2019 08:07 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ? > > Dear Matthias, > > Of course, high completeness is better than low completeness. > But as long as your low resolution is pretty much complete, there is no such > thing as "too low completeness" at high resolution. Each reflection adds > information to the map, and serves as a restraint in refinement. > > best, > Kay > > > On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke > <oebbe...@staff.uni-marburg.de> wrote: > >> Dear ccp4 Bulletin Board, >> >> I collected a dataset at a synchrotron beamline and got the statistics >> (CORRECT.LP) after processing (using xds) shown in the attached >> pdf-file. >> >> Do you think this dataset is usable, due to its low completeness? As >> you can see in the attached file the completeness is just 50% in the >> highest resolution shell, whereas the I over Sigma is above 2 and also >> the CC 1/2 (80%) and the R factors (36.8%) have reasonable values. >> Furthermore the overall statistic are good regarding R factor, CC 1/2 >> and I over Sigma. The only problem seems to be the completeness. If I >> would set the cut-off at a lower resolution to get good completeness, I >> would throw away nearly half of my reflections. >> >> I'm happy to here your opinion. In Addition to that: The space group is >> orthorhombic and the dataset was collected over 120° using fine slicing >> (0.1°). >> >> >> Best regards, >> >> Matthias Oebbeke >> >> >> -- >> Matthias Oebbeke, M.Sc. >> Research Group of Professor Dr. G. Klebe >> Institute of Pharmaceutical Chemistry >> Philipps-University Marburg >> Marbacher Weg 6, 35032 Marburg, Germany >> Phone: +49-6421-28-21392 >> Mail: oebbe...@staff.uni-marburg.de >> www.agklebe.de >> >> ######################################################################## >> >> 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 > > ######################################################################## > > 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
