My preference is to use the term 'observed' for reflections whose intensities have been integrated, and the term 'informative' for those that satisfy some statistical criteria of being useful for structure determination. Programs like Truncate have hidden criteria of rejecting some observed reflections from the informative group, so this issue has been around for a long time. For a typical, properly done data collection, resolution limit is a widely used criterion of informativity. For anisotropic diffraction, a single number is definitely not a proper way to define the resolution limit. So we need something like signal-to-noise ratio cut-off to define a better equivalent of the resolution limit. The question is what we mean by signal-to-noise: it can be individual (unique/merged) reflection values (a wide-spread practice in small molecule crystallography, and for a good reason) or either signal, noise, or both of them, which are group averages rather than individual estimates, Personally, I prefer a ratio of an average signal to an individual uncertainty as a criterion that defines the informativity limit equivalent to a resolution cut-off. The second aspect of the issue is what value of the signal-to-noise ratio (however defined) should be the limiting criterion. The value around 2 represents a limit of what is 'fully' informative, and, as has been discussed, lower values of signal-to-noise provide some extra information. Around the ratio of 1, the value of the information becomes minimal.
So for me, there are 2 types of data completeness: one, in terms of Bragg's condition, which defines if we missed part of reciprocal space during the experiment; and second, in terms of what is informative for structure solution. The second type will typically be low for resolution range close to the limit in the case of anisotropic diffraction. There is, therefore, nothing wrong in terms of how the experiment was done, if such completeness is low; on the other hand, the first type can tell us whether the experiment could be done better. So there are good reasons to report both types of completeness in the publication and in the deposit, even if there is no such custom yet. Zbyszek Otwinowski > There is some disagreement on terms used to deposit data. We need a > definition and an algorithm > for each definition. > > "Unique Reflections" > > My definition is all the possible reflections out to the high resolution > reported not related by symmetry. > Where can I find this? The .mtz contains a list of all HKL calculated to > the highest resolution. Usually, we > are not able to measure all these diffraction spots due to limits of the > detector, mechanical limits, crystal > orientation, etc. > > 'Total reflections' > The depositions server asks for total reflections. I assume it wants only > those unique reflections we were able to > collect, regardless of the sigma cut off. These are called 'observed'. The > total we use in refinement will be a subset > of the 'unique observed' that are cut on sigma. However, some > crystallographers believe that we should not cut > on sigma since some of the intensities may in fact be zero. Is this a > question for both the Refmac and Phenix people? > > Please give us some guidance and maybe a reference or two that we can use. > > > -- > Kenneth A. Satyshur, M.S.,Ph.D. > Senior Scientist > University of Wisconsin > Madison, Wisconsin 53706 > 608-215-5207 > Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
