The files were written on the axes the space-group search named, which for
P2221/P21212 puts the unique axis wherever the a<b<c indexing put it (a 52.51
87.87 137.72 crystal came out P 2 21 21 where XDS writes 87.87 137.72 52.51
P 21 21 2), and a reference MTZ was matched in the data's frame: on permuted
axes its free-R flags landed on unrelated reflections while the log reported a
high matched count.
- New CrystalSetting (scale_merge): changes of basis between settings of one
lattice (cell, group, index operator, basis matrix), the {-1,0,1} det +1
candidates (CellMappingOperators, moved from ModelValidation), MetricViolation
(moved from Rugnux), ChooseOutputSetting and SeatGroupByAbsences.
- Output setting: after every decision the merge, the integrated reflections
(unmerged MTZ), the P1 cross-check, the lattice and the _process.h5 reindex
matrix are relabelled into the ITA standard setting - or, in priority order,
a reference MTZ's, a fitting model's, the -C axis order, a non-standard -S
symbol's. Free-R flags are drawn again on the written axes. Reported as
SETTING_OPERATOR / SETTING_SOURCE.
- Reference MTZ: the group is kept in its setting; after the merge every cell
mapping onto the reference cell (times the twin laws) is scored by the
reference CC, the best is re-seated and re-merged, and the free flags are
inherited only where CC >= 0.5 over >= 50% of the reference range
(REFERENCE_MISMATCH otherwise; --mode scale gates the same way).
REFERENCE_OPERATOR / _CC / _MATCHED_FRACTION / _FREE_FLAGS_INHERITED.
- -S: a fixed group is put on the axes its absences name before merging
(SeatGroupByAbsences), fixing -S 18 on a cell whose pure axis is not c.
- --model: a model in another setting is now a claim the null tests; where it
fits, the data are written in its setting and the validation is remade on
those axes (KeepModelVerdict carries the decisions over).
Tests: [setting] (synthetic #18/#17/I222/C222/c-unique P21/C2 beta/I2->C2/P1,
-C and -S order, absence seating, permuted reference with flags).
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
