RUGNUX_ADVANCED's --model page described the rigid body alone. It now says how the unified flow
places a model: an experimental model by the rigid body, checked against its null in the answer's
or the twin hypothesis' merge, and by molecular replacement where it is not placed; a prediction
straight to molecular replacement; --mr skipping the rigid body; MODEL_PLACEMENT. It says what a
placed model may change in <prefix>.mtz (the hand, and from the rigid body an indexing-ambiguity
reindex) and that another group or the twin subgroup the model chooses goes to <prefix>_mr.mtz/.cif
with <prefix>_mr_model.pdb/.cif. --mode scale places by the rigid body only (no molecular
replacement, --mr refused); a full run does molecular replacement on serial stills too (checked:
a stills run with a predicted model reports MODEL_PLACEMENT= MR). The options table gains --mr
and the --model row the fallback.
RUGNUX_INTEGRATION no longer says rugnux does no molecular replacement, and ACKNOWLEDGEMENT names
--model beside --mr for predicted models.
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
5e916fe120
