The per-image reference/model choice of indexing ignored the crystals' refined cells. On a
pseudo-merohedral cell, where at least 90% of the crystals' cells fit the run's cell better as
indexed than after a twin law, the cells decide that law - the rule the data-only resolution
already uses (AnchorOnCells, factored out of ResolveReindexReferenceFree and shared). The resolver
now keeps each image's CC per indexing (IntegrationOutcome::reference_cc); before the stills
merge, AnchorReferenceReindex puts every image back as indexed, applies the cell rule, and lets
the reference choose only among the indexings left open. Exactly merohedral lattices (no metric
signal) are unaffected.
Still battery (REFMAC 0-cycle R-free, model before -> anchored; data-only in brackets):
pal90 0.1883 -> 0.1834 (0.1832), alvra213 0.2073 -> 0.2011 (0.2013), alvra213_int16
0.2081 -> 0.2021 (0.2024); euxfel83 0.2037, euxfel152 0.2452, sacla237, lcls222 unchanged;
lcls242_t 0.2847 -> 0.2952 (0.2942): there the model had moved about half the crystals against
cells that decide all three laws (96/96/100%).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 85c804676ffd15ffd66e2ba05928000d6f4e765f)
Where the space group is given (-S) and its lattice admits alternative indexings, a stills run without
-z or --model used to merge the crystals' random indexings together (and warned). The crystals are now
made consistent with each other before anything is scaled (ReferenceFreeReindex): each takes the
indexing in which it agrees best with all the others (Brehm & Diederichs 2014), agreement being the
sum over shared reflections of the products of shell-normalised, per-crystal standardised intensities,
weighted by 1/(1+(sigma/sd)^2). The sum over all pairs is (|M|^2 - const)/2 for M the running sum, so a
pass over the crystals is one pass over the reflections rather than over all pairs: coordinate ascent,
four seeded starts, stop when <= 1 crystal in 1000 moves, the overall relabel that moves the fewest
crystals. Deterministic (fixed summation order, sequential passes).
A twin law of a pseudo-merohedral cell whose axes differ by a few per cent is decided by the crystals'
own refined cells, which the indexer has already used: where >= 90% of the crystals' cells fit better as
indexed, those crystals are anchors and only the others are decided by the intensities. Without this,
two public sets got worse (pal90 R-free 0.183 -> 0.207, lcls242_t 0.296 -> 0.350).
With a reference or model the per-image choice stands; the same resolution runs as a check, reported as
AMBIGUITY_DATA_DISAGREES. New report keys (section 2): INDEXING_AMBIGUITY_RESOLVED, AMBIGUITY_CRYSTALS,
AMBIGUITY_REINDEXED, AMBIGUITY_SEPARATION_SIGMA, AMBIGUITY_DECIDED_FRACTION (+ AMBIGUITY_TIME_S, dev).
--mode scale is not changed.
Still battery, no --model (R-free, REFMAC 0-cycle against the deposited model; before -> after; with
--model for comparison): euxfel83 0.321 -> 0.207 (0.204), euxfel152 0.346 -> 0.257 (0.245), alvra213
0.209 -> 0.201 (0.207), alvra213_int16 0.210 -> 0.202 (0.208), pal90 0.183 -> 0.183 (0.188), lcls242_t
0.296 -> 0.294 (0.285); controls sacla237 / lcls222 unchanged (no ambiguity, no-op). The step takes
0.2-1.6 s on 2.7k-54k crystals; synthetic 64k crystals x 200 reflections 0.5 s.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 80d378a1fe92364fd5b99a17f5c9ee8498412d36)
leonarski_f