A new page, RUGNUX_MODEL_AND_REFERENCE.md, beside the other rugnux pages in the toctree and
linked from RUGNUX.md and the --model section of RUGNUX_ADVANCED.md. It lists every option that
brings in a model or reference data (--model, --mr, the PAE file beside a prediction, -z and
--reference-column, -S, -C, --force-rotation-lattice, --report-resolution), sorts every decision
into data-only, model-informed label in <prefix>.mtz (hand past the anomalous veto, indexing
ambiguity, setting), model-driven separate files (<prefix>_mr) and report-only statistics, walks a
--model run step by step, says exactly where a model can touch the space group and what guards it
(the null, the anomalous veto, the indexing margin, the MR rules, the wrong-model battery step),
and describes the free set and model bias (a deposited model's R-free on rugnux's own test set is
not cross-validated; -z with the PDB's structure factors inherits the depositor's set). Includes the
one pre-merge use of a model: serial stills with -C/-S, where it breaks the per-image indexing
ambiguity. Documentation only; behaviour as merged in rc175 (7ed970503).
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3
leonarski_fandClaude Opus 5.5
8b43cce9eb
