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I see no problem with saying that the model was refined against every spot on the detector that the data reduction program said was observed (and I realize there is argument about this) but declare that the "resolution of the model" is a number based on the traditional criteria. This solution allows for the best possible model to be constructed and the "buyer" is still allowed to make quality judgements the same way as always. Dale Tronrud On 4/18/2014 5:22 PM, Lavie, Arnon wrote: > Dear Kay. > > Arguably, the resolution of a structure is the most important > number to look at; it is definitely the first to be examined, and > often the only one examined by non-structural biologists. > > Since this number conveys so much concerning the > quality/reliability of the the structure, it is not surprising that > we need to get this one parameter right. > > Let us examine a hypothetical situation, in which a data set at > the 2.2-2.0 resolution shell has 20% completeness. Is this a 2.0 A > resolution structure? While you make a sound argument that > including that data may result in a better refined model (more > observations, more restraints), I would not consider that model the > same quality as one refined against a data set that has >90% > completeness at that resolution shell. > > As I see it, there are two issues here: one, is whether to include > such data in refinement? I am not sure if low completeness > (especially if not random) can be detrimental to a correct model, > but I will let other weigh in on that. > > The second question is where to declare the resolution limit of a > particular data set? To my mind, here high completeness (the term > "high" needs a precise definition) better describes the true > resolution limit of the diffraction, and with this what I can > conclude about the quality of the refined model. > > My two cents. > > Arnon Lavie > > On Fri, April 18, 2014 6:51 pm, Kay Diederichs wrote: >> Hi everybody, >> >> since we seem to have a little Easter discussion about >> crystallographic statistics anyway, I would like to bring up one >> more topic. >> >> A recent email sent to me said: "Another referee complained that >> the completeness in that bin was too low at 85%" - my answer was >> that I consider the referee's assertion as indicating a >> (unfortunately not untypical case of) severe statistical >> confusion. Actually, there is no reason at all to discard a >> resolution shell just because it is not complete, and what would >> be a cutoff, if there were one? What constitutes "too low"? >> >> The benefit of including also incomplete resolution shells is >> that every reflection constitutes a restraint in refinement (and >> thus reduces overfitting), and contributes its little bit of >> detail to the electron density map. Some people may be mis-lead >> by a wrong understanding of the "cats and ducks" examples by >> Kevin Cowtan: omitting further data from maps makes Fourier >> ripples/artifacts worse, not better. >> >> The unfortunate consequence of the referee's opinion (and its >> enforcement and implementation in papers) is that the structures >> that result from the enforced re-refinement against truncated >> data are _worse_ than the original data that included the >> "incomplete" resolution shells. >> >> So could we as a community please abandon this inappropriate and >> un-justified practice - of course after proper discussion here? >> >> Kay >> >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlNRz14ACgkQU5C0gGfAG138HwCfYbUXb5MgQvC/8iCftiuuP1pn H0AAn24ej2FSBxbNbndjnHoJ/xAKCitK =Xh7C -----END PGP SIGNATURE-----
