I am aware that some programs report interesting numbers. In addition to what Andrew wrote about resolution cutoffs and "truncated" reflections, I'd like to mention another issue with systematically absent reflections.
The number of observations or reflections that come from an integration program are fed into a scaling program. However, the integration program may use a different space group than the scaling program. I am aware that in HKL systematically absent reflections are counted as observations when given to the scaling program SCALEPACK, and are reported in the log file as a unique reflection, but do not appear in the output *.sca file. For example, when the integration program uses spacegroup P4 to integrate, then the user scales in spacegroup P4(1)2(1)2. What happens to the (0 0 5), (0 0 6), (0 0 7), (0 0 9), (0 11 0), and other systematically absent reflections in P4(1)2(1)2 that are passed from the integration program to the scaliing program? I can tell you that they disappear from the output file, but appear in the "total number of observations" in the log file. So if the input file to scaling has 169 systematically absence observations that when reduced to unique reflections yield 69 unique reflections, then SCALEPACK will report 169 extra input observations and 69 extra output unique reflections than are present. Jim ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Naveed A Nadvi [nnad2...@uni.sydney.edu.au] Sent: Sunday, April 15, 2012 3:06 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] unique reflections vs unique observations Dear CCP4 users, I am a bit confused about the use of these terms in regards to structure refinement statistics. When I process my data with SCALA, the program outputs statistics in terms of "total and unique numbers of observations". However, when I use the MTZ files with REFMAC, the final PDB file has "number of reflections". These values are of similar magnitude, but not identical. The issue is even more complicated when I look at tables of statistics between different journals. Authors often report unique reflections or unique observations. My questions are: 1) Are these two terms interchangable? 2) Are they relevant to the different stages of processing (e.g. data collection vs structure refinement)? 3) How do I rationalize the difference between the two values? I have read some of the widely used textbooks, but I am still confused when looking at publications. Any comments would be highly appreciated! Kind regards, Naveed Nadvi Faculty of Pharmacy, University of Sydney.
