leonarski_fandClaude Opus 4.8
95af137146
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>
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.