Dear all, After upgrading XDS from build date 20170601 to 20171218, I am experiencing severe degradation of apparent data quality reported by CORRECT for certain data sets. Following first indications of issues with a slightly problematic candidate, I went back to a previously very well-behaved test case with diffraction extending beyond 1.1 A. Using the same input with both program versions, statistics are not too different out to approx. 1.6 A, but become more and more divergent in outer shells. These are the values for the highest-resolution shell (1.10--1.16 A):
20170601: I/sigI = 1.80; Rmeas = 59.9 %; CC(1/2) = 82.0 % 20171218: I/sigI = 0.14; Rmeas = 506.4 %; CC(1/2) = 5.8 % The refined cell constants are unreasonably different as well. Obviously, something is going awfully wrong here, presumably related to errors in geometry parameters (which are expected to become increasingly detrimental with decreasing dmin). As it turns out, geometry refinement behaves differently in the latest version of XDS: most notably, IDXREF no longer refines the detector distance by default. This is significant in this case, as in version 20170601 the distance would shift by as much as 1.3 mm, resulting in successful integration and scaling. Unfortunately, re-adding POSITION refinement into REFINE(IDXREF) does not help, and even having it in all refinement scopes (IDXREF, INTEGRATE, CORRECT) only yields a limited improvement of CORRECT statistics. It is worth noting that examination of a dataset from an unrelated crystal (dmin = 1.4 A) did not reveal such enormous differences -- in this case, however, the shift in detector distance applied in the old version of XDS was quite small (0.2 mm), which, together with the lower resolution, explains the absence of large discrepancies. To sum up, I suspect that, due to recent changes to the XDS code, the refinement of geometry parameters is now overly restrained, resulting in drastic problems in cases where the detector distance is not as precise as desirable (and even more so at very high resolution). For such datasets, the new version appears to be essentially unusable (at least within the parameter space I have tested), and even in modest cases may often be inferior to the previous one. Is there an option to revert to the former behaviour? Best regards Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
