I don't think "observed" means all the reflections that were integrated, becasue one of the other parameters is the criterion for a reflection to be considered "observed", so that "observed" is a subset of "all". Here are some lines I saved from an adit2 session (some years back, but I believe it was the same in a recent deposition) I don't think the questions fit very well the way we collect and process data today, but I think most of these are optional. What I called Rsym should probably be called Rmerge, from merging frames not merging crystals.
Observed criterion sigma(F) >> null << Observed criterion sigma(I) -3 Resolution (high) 3.000 Resolution (low) 42.68 Number unique reflections (all) >> ? << Number unique reflections (observed) 141782 Percent possible (observed) 91.8 R-merge I (observed) ? R-sym I (observed) 0.124 On 07/15/2014 11:26 AM, Kenneth A. Satyshur wrote:
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 highest 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 the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
