An external reference MTZ is a poor per-image scale reference: it is a different crystal/dataset,
so scaling against it injects cross-dataset systematics rather than removing per-image scale error
(measured: reference-scaled R-free 0.410 vs self-scaled 0.388 on OCP; 0.378 vs 0.350 on LOV). Its
real value is fixing the cell/space group, breaking the merohedral indexing ambiguity, reporting
CCref and providing the R-free test set - none of which need it to be a scale anchor.
Make that consistent across both workflows:
- Stills: the per-image pass (ScaleImage) now uses the reference ONLY to break the indexing ambiguity
(once, for good), not to fit G. Scaling self-references at the post-measurement merge for every run,
whether or not a reference is given (Rugnux + rugnux_cli --scale).
- Rotation: ScaleImage no longer scales against the reference either (it was dead code - RotationScaleMerge
recomputes the per-frame scale, so the reference never actually moved the result). Rotation resolves
the ambiguity globally (ChooseReindex / ReferenceIntensityCC) and self-scales in RotationScaleMerge.
- A reference-as-scale mode, if ever wanted, would be a dedicated later step, not this per-image pass.
Validated: OCP CCref 56.5%->64.6%, R-free 0.400->0.393 (honest 2.36 A cutoff instead of a reference-
propped 1.5 A); LOV CCref 88.3%->90.1%, R-free 0.336->0.331 with more reflections; rotation lyso_ref
with the reference gives ISa 17.8 == de-novo 15.6 (same 15975 reflections, CC1/2 99.8%) - the reference
demonstrably does not touch rotation scaling, only cell/SG + ambiguity + CCref.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8
95af137146