Providing both a unit cell (-C) and space group (-S) silently broke the de-novo
indexers (FFT/FFTW) -> 0% indexing, while each flag alone worked. Root cause: the
`sg && GetUnitCell()` branch fed the indexer's raw lattice straight into
symmetry-constrained refinement. FFBIDX returns the lattice already in the
reference setting, but FFT/FFTW return an arbitrarily-oriented Niggli-primitive
cell; enforcing the crystal system on its mis-assigned axes rejects every frame.
Fix: for de-novo indexers only, reduce the lattice to the conventional setting
(LatticeSearch) before refinement. FFBIDX keeps using its raw lattice as-is, so
it is byte-identical to before (no regression). niggli_class stays unassigned (0)
in this branch - it is a property of the primitive cell incl. centering, which
LatticeSearch cannot recover from a user-supplied (possibly centered, e.g. C2)
cell. A proper primitive-cell indexing path (CrystFEL-style) is deferred.
Validation (lyso, -C79,79,38 -S96):
crystal 2 FFT : 0% -> 94.9% (CC1/2 95.8, CCref 92.7) = de-novo quality
crystal 2 FFBIDX: 71.4% (CC1/2 94.6) - byte-identical
jet FFBIDX: 27.2% (CC1/2 91.9) - byte-identical
(Jet FFT stays 0% - that is a separate, still-open issue: de-novo finds no
consensus on the weak serial-still frames, 0% even without -S; to investigate.)
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8
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