The batteries now score the deposited model against a merge one way: model_check.py, REFMAC's first
cycle before any shift (bulk solvent and anisotropic scale by default), the depositor's free set,
d_min_used = max(ours, deposited), compared against the deposited data through the same protocol.
- model_check.py: the restrained-refinement protocol is removed (refine, refined_shared,
rename_misfit_ligands, REFINE_CYCLES, the refined parameter, --no-refine). Both data sets are now
scored on their common reflections only, so a low-resolution or anisotropic cut of either applies
to both (measured on three still sets: <= 0.001 change).
- battery.py / paper_plots.py: refmac_refined_* and refmac_refined_ratio are gone; refmac_rfree_ratio
is the headline; paper_plots draws the first-cycle pair only (--rfree removed).
- still_battery.py: dimple is replaced by model_check.check on the same p.mtz. R_free rugnux is
rfree_depflags, the target is rfree_depdata (no longer min(dimple, published)); the published
R-free stays as an information column. The dimple cache, free-flag writer, deposited-MTZ writer
and the reference verb are removed. This also retires dimple's freerflag COMPLETE renumbering,
which scored R-free on depositor work reflections whenever our merge had hkl the deposition
lacks (model_check carries the depositor's flags per hkl and marks ours-only hkl as work, and
with the common-hkl restriction there are none). `report RUN --out DIR` rescores an older run's
merges without rerunning rugnux.
Refinement cost about 6.4 h per full rotation battery; the 0-cycle check takes seconds per set.
Verified: 9V3D still merge reproduces the 0-cycle common-hkl numbers (0.2461 ours, 0.2367 deposited).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
leonarski_fandClaude Opus 5.5
4d8c2cc031