rugnux --mode refine --model model.cif -o out data.mtz
The input is an MTZ or a structure-factor mmCIF, gzipped or not, by content
(writer/RugnuxReflectionFile: parsing in the file layer, the library reads no file). Columns are
found, not named: F/SIGF-like amplitudes (calculated amplitudes and map coefficients passed over),
else intensities made into amplitudes by French-Wilson, else the mean of the anomalous pairs; the
free set from a FreeR_flag-like column (0 the test set, or the minority value), else rugnux's own
5 % set. RunRefineOnly (rugnux/RugnuxRefine) runs RefineModel; the outputs are --refine's
(_refined_model.cif, _refined_maps.mtz, _blobs.json) and a report with the REFINE_ keys, the input's
REFINE_FRENCH_WILSON / REFINE_FREE_FLAGS, and every term of the start score under REFINE_SCORE_
(also in --refine's section). --refine-score-only scores the model as given; --refine-d-min cuts
the resolution.
tools/battery/refine_parity.py runs REFMAC 5.8 at 0 cycles and rugnux --refine-score-only on the
same files and prints the terms side by side, with R by resolution from both programs' model
amplitudes on the same reflections.
Tests: [refine_only] - column choice (observed over map coefficients, intensities, 1-marks-free
flags, no flags, no usable column), an MTZ read from its bytes, and the mode end to end on a
synthetic cell (French-Wilson, generated flags, score-only, the report keys).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 63ee830c39c988588cffb8c9d4638a678815ec2c)
(cherry picked from commit d7397311e6ce0d3bb37ac91e8973b6052e38589f)
