Dear Phenix/CCTBX developers, iotbx/merging_statistics.py is used by phenix.merging_statistics, phenix.table_one, and so on. By upgrading phenix from 1.10.1 to 1.11, merging statistics-related codes were significantly changed. Previously, miller.array.merge_equivalents() was always called with argument use_internal_variance=False, which is consistent with XDS, Aimless and so on. Currently, use_internal_variance=True is default, and cannot be changed by users (see below). These changes were made by @afonine and @rjgildea in rev. 22973 (Sep 26, 2015) and 23961 (Mar 8, 2016). Could anyone explain why these changes were introduced? https://sourceforge.net/p/cctbx/code/22973 https://sourceforge.net/p/cctbx/code/23961 My points are: - We actually cannot control use_internal_variance= parameter because it is not passed to merge_equivalents() in class filter_intensities_by_sigma. - In previous versions, if I gave XDS output to phenix.merging_statistics, values calculated in the same way (as XDS does) were shown; but not in the current version. - For (for example) phenix.table_one users who expect this behavior, it can give inconsistency. The statistics would not be consistent with the data used in refinement. cf. the related discussion in cctbxbb: http://phenix-online.org/pipermail/cctbxbb/2012-October/000611.html Best regards, Keitaro