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leonarski_fandClaude Opus 5 dc71cb7299 rugnux: keep the P1 merge, so a wrong space group is recoverable

A de-novo rotation run merges in P1 to search for the symmetry, adopts a
group, and then overwrites that merge with the in-symmetry one. If the
adopted group is wrong the user has no route back: every file the run
wrote, and every statistic in them, is computed in the group that was
assumed, so nothing in the output says the choice was wrong and the only
way to a different answer is to process the images again.

Merge the same integration once more in P1 after the run's own files are
written, and put it beside them as <prefix>_P1.mtz. From it the space
group can be re-determined and the data re-merged, re-solved or
re-refined in any subgroup - measured end to end on three crystals:
POINTLESS reads the file, recovers the group, and AIMLESS re-merges it,
reproducing rugnux's own merged intensities at CC 0.9965 where the two
agree. On one of the three it recovered the deposited/XDS group where
this run had under-called the screw axis.

The merge is the full one - correction surfaces fitted, ice rings and
near-tangential observations kept, whole resolution range - not the
deliberately degraded merge the space-group search itself runs on, and
it is what `rugnux --mode scale -S P1` produces from a _process.h5. That
route already existed but needs a _process.h5, which a merging run does
not write, so it only helped a user who had foreseen the problem.

Every de-novo rotation run writes the file, including one whose search
concluded P1 and where it therefore repeats the merged output byte for
byte. Whether a file exists must not depend on what the pipeline
decided: a script harvesting results would otherwise have to reproduce
the search's decision to know whether to expect it, and a missing file
would not separate "the run chose P1" from "the run failed".

A user-fixed -S writes nothing, and that condition is not a pipeline
decision. With a group fixed, prediction rejects that group's centring
absences (IndexAndRefine.cpp:499-506), so those reflections are never
integrated; a P1 merge built from such a run would be missing whole
centring classes and would mislead rather than merely be smaller.

Cost, median of five paired runs read off the log timestamps (the box is
shared, so end-to-end wall time is noise): +0.32 s of 4.2 s, +2.18 s of
31.4 s, +0.19 s of 17.9 s, +0.66 s of 15.9 s - 1 to 8% of a run. The
file is 1.6x the merged MTZ on a monoclinic crystal and 30x on a cubic
one, where the merged MTZ is tiny; it is well under the unmerged export
in every case measured, and 0.02 to 0.6% of the raw dataset.

Rotation only for now: the stills merge re-fits per-image scales and
per-reflection partialities onto the integration outcomes, and
_unmerged.mtz is written from those afterwards, so on stills this extra
merge alters a file that is the run's own output. Fixing that means
running the cross-check below the unmerged export, which needs the merge
lambda hoisted out of its block; deferred, since rotation is what the
online pipeline processes. On rotation the merged .mtz, .cif, .hkl,
_image.dat, _unmerged.mtz and _unmerged_partials.mtz are all
byte-identical with and without this change, including on a run whose
search returns P1.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01T3yNBXk4wKdMZy1ak2NY7f

2026-08-30 12:36:49 +02:00