The one outright falsehood: the R-free convention paragraph in
RUGNUX_INTEGRATION.md still described the pre-flip FreeR_flag numbering
(0 = work, phenix/CNS) and told REFMAC5 users to pass FREE 1 - on a
current file that keyword designates the 95% working set as free and
REFMAC stops. The file has carried 0 = free (CCP4) since the flip; the
paragraph now says so, the keyword is gone from the worked script, and a
note keeps the old error message findable for files written before it.
A contradiction within RUGNUX_ADVANCED.md: the --mode scale section said
the mode never reindexes the reflections it writes, while the indexing-
ambiguity section (correctly) said --mode scale --model does resolve a
rotation ambiguity. The code adopts the model's frame before writing, so
the former now agrees with the latter, and says what genuinely cannot be
repaired: a stills _process.h5 integrated without a reference.
Half-updated model-validation prose: the pages that predate the
hypothesis gate still described --model deciding the enantiomorph and
the indexing unconditionally. Every such statement (quick start,
tutorial, the ambiguity table and bullets, the validation section) now
carries the gate: the model decides nothing unless it beats the null of
its own random placements, and the indexing choice must also beat the
null's margin. The map names now say sigma_A-weighted 2mFo-DFc/mFo-DFc.
Missing files: the tutorial's output-file list did not mention the
--model outputs at all; it now lists the maps, the map-coefficient MTZ,
the anomalous map and the placed model in both formats, and points out
that <prefix>.cif is reflections while <prefix>_model.cif is
coordinates. _model.pdb is added beside _model.cif everywhere the placed
model is described, with the PanDDA/dimple reason it exists.
Undocumented indexing behaviour: the axis-harmonic spot-count arbiter
and the default-on short-axis second hypothesis existed only as
changelog lines; CPU_DATA_ANALYSIS_INDEXING section 6 now describes
both, and the --fft-min-unit-cell texts no longer claim a crystal below
the 10 A floor cannot be indexed at all.
Small corrections in RUGNUX_REPORT.md: sweep-quality warnings live in
section 11, not 9; JFJOCH_DATASET_SETTINGS carries the poni_rot*_rad
angles too whenever any is non-zero. The tutorial's post-refine sentence
now states the real commit bounds (distance under 1%, beam within 15 px
of the header or the run's own measured centre, whichever is nearer)
instead of "restrained toward the header", which f98442077 made stale.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
b971f99b53
