Hi Huw, When I was at the workshop, I have to admit that after ccp4i2 refused to do it I switched to Phenix and used phenix.reflection_file_converter! It would be better if i2’s reindex or change spacegroup task didn’t refuse, and I guess this might improve after the overly-zealous consistency checking is relaxed, or cad could be used following your suggestion.
As for how to report this in a publication, we actually ran into this when working on a Hyp-1 complex structure with Mariusz Jaskolski and Zbyszek Dauter, where the crystals were apparently perfectly tetartohedrally twinned. The apparent space group was some variant of P422 (which is how the data were processed and merged) but the true space group was identified as one choice of C2. Merging in the correct space group gave only 73% completeness, but the statistics for the data processed in higher symmetry were very similar so the expanded data set was used and deposited (https://doi.org/10.1107/s1399004713030319). Statistics for processing in both space groups were presented in Table 1. Best wishes, Randy > On 23 Feb 2024, at 13:45, Huw Jenkins <h.t.jenk...@me.com> wrote: > > Hi Randy, > >> On 23 Feb 2024, at 11:49, Randy John Read <rj...@cam.ac.uk> wrote: >> >> Why would we want to impose an arbitrary restriction on users for this >> relatively common scenario. > > If the user has the unmerged data this can be imported into CCP4i2 via the > data reduction task and merged in P1. How would you expand the merged data to > P1 - using cad from a script? Perhaps this should be made possible in CCP4i2 > after the merged data were imported. i2 already has a "Reindex or change > spacegroup" task (using POINTLESS) but it won't do this: > > "FATAL ERROR: > Specified SPACEGROUP P1 must belong to same crystal system and point group > as the input space group P 41 21 2" > >> >> Note that this kind of confusion between twinning and true symmetry will >> mostly arise when the twin fractions are close to equal. Then: a) the >> twin-related intensities should really be measurements of the same thing, >> and you get more precise data by making them equal; b) the superimposed >> diffraction patterns will obey the higher symmetry, although the spots might >> start to split at higher resolution. >> >> I would also argue that, if the twin fractions are experimentally >> indistinguishable from being equal, processing in higher symmetry and >> expanding the data to the correct lower symmetry is the correct approach to >> take for your final data set. > > That's a fair comment. In that case would you then report the merging > statistics for the higher symmetry data in "Table 1" and note that the merged > data were subsequently expanded to the correct lower symmetry? > > > Huw ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
