A _process.h5 was internally inconsistent whenever the space group re-seated
the lattice. The per-image reflections and lattices go to file as each image
is processed, but the conventional setting is only chosen afterwards, so the
file kept pre-reindex indices beside a post-reindex cell. Measured on an
affected dataset, max|d_file - d(hkl, stored cell)| was 18.6 A. --mode scale
then compared each frame's lattice against the stored cell, found none of
1800 acceptable, rejected every observation and died in the merge with
"resolution calculation failed".
/entry/MX/reindexMatrix now carries M with hkl_cell = M . hkl_written, and
the reader applies it, so everything it hands out is in the setting of
/entry/sample/unit_cell. Absent means the identity, so a file written before
this reads exactly as before. On the affected dataset M comes out
[[1,1,0],[0,1,1],[1,0,1]], det 2 - the primitive-to-body-centred basis its
volume ratio implied - and the same measure falls from 18.6 A to 1.8e-5.
Writing the reflections in the final setting instead was rejected: the
per-image writer is shared with the broker, which streams and cannot buffer a
run; and h,k,l, predicted_x/y and the per-image lattice are one consistent
statement about one image, which retro-editing the indices would silently
break.
Two things turned up while fixing it. There are three re-seat sites, not one
- the space-group search's own centred-lattice test re-seats too, and logged
nothing - so the matrix composes over all of them. And the space group itself
was never written: it was set only on the arm that searches, while a two-pass
rotation run reuses pass 1's group and takes the other arm, so the canonical
file carried a cell but no group and --mode scale merged in P1.
--mode scale now reproduces --mode mx on the affected dataset: same space
group and cell, 39329 unique reflections both, 100% of reflections common,
CC 0.99985, sum|dI|/sum|I| = 0.0081. The residual is three reflections in
11.09 M crossing an ice-band edge, because mx carries the integrator's d and
scale recomputes it from the cell. An unaffected dataset is byte-identical in
.mtz, .hkl and .cif.
An older affected file still cannot merge - M is not recoverable from it -
but now says so in 51 s, naming both cells and the -S/-C override to use,
instead of failing inside the merge.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P
leonarski_fandClaude Opus 5
db908c6ec1