One --model now does the right thing by itself:
- A prediction (AlphaFold/ModelCIF, read from the file) goes straight to molecular replacement.
- An experimental structure is placed by the rigid body as before. The null now runs on every
--model run (no NOT_TESTED): "placed" = the fit beats its null (4.51 sd) in the answer's merge
or in the twin hypothesis' merge. Placed: behaviour unchanged (hand and reindex may go into
p.mtz); a subgroup the model fits and prefers is written as <prefix>_mr.
- Not placed (or no crystal cell): molecular replacement with the experimental-model path. It may
relabel the hand into p.mtz past the anomalous veto, never reindexes; another group or the twin
subgroup goes only to <prefix>_mr. Maps, R-free and CC come from validating the MR placement with
every decision switched off; MODEL_FIT stays the rigid body's verdict.
- The twin hypothesis' merge is made in memory with a model where a metric re-ask promoted the
group or the model's group has fewer rotations than the adopted one; written and reported only
where the model chooses it.
- --mr is kept as "--model, searched for by MR straight away".
- Report: MODEL_PLACEMENT= RIGID_BODY|MR|NOT_PLACED, MODEL_DECISIONS_TAKEN gains MR_ENANTIOMORPH,
MODEL_CHOICE_FILE_PREFIX/SPACE_GROUP; the MR keys move into 5. MODEL VALIDATION; MODEL_FIT absent
where no rigid body ran. MR NOT_PLACED is never a warning.
- Battery wrong-model step: check (c) also fails a wrong model placed by MR.
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
d0d225cb99
