leonarski_fandClaude Opus 4.8
2d7ddb1b67
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Serial stills index each crystal in one of the merohedrally-equivalent hands at random, so the ambiguity must be broken per image, not globally as the rotation path (RotationScaleMerge/ChooseReindex) does. When an external reference MTZ is supplied, IndexAndRefine::ReferenceIntensities now builds the per-image scaler with resolve_ambiguity=true: for each image it picks the reindexing (identity or a twin law from ReindexAmbiguityOperators) whose partiality/Lorentz-corrected intensities correlate best with the reference, then reindexes that image's reflections before scaling. Off for the self-merge scaling pass (no trusted reference to break the tie). Holohedral crystals (no twin law, e.g. lysozyme P43212) are a no-op. Validated on OCP P3221 (twin law -x,-y,z) with a 7ZSJ reference: CCref 24->48% and CC1/2 24->64% at 30k images; CC1/2 96.9% / CCref 76% at 150k. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>