leonarski_fandClaude Opus 5
b971f99b53
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
4.1 KiB
What a rugnux run does
The map of a run, in the order it happens — one paragraph per stage, each linking into the data-analysis reference where the algorithm lives. The walk-through is a rotation run with the defaults; stills differences are at the end.
Open the dataset. The geometry, wavelength and goniometer come from the file (What rugnux reads). A goniometer axis makes it a rotation run, none makes it serial stills — nothing is asked of the user.
Pre-scan. A projection of the first frames (60 by default) finds the beam-stop shadow and masks it (§1.5), measures the beam centre from the isotropy of the scattered background and compares it with the file's (§1.4), and reads how wide this crystal's spots are, which sets the integration radius (§9.5).
Spots. Every image is decoded — on the GPU straight from the compressed chunk (§0) — and one fused pass computes the azimuthal profile and finds the spots against each image's own per-resolution-ring noise (§2–§3). The ice-ring score is read off the same profile.
Indexing. The spots of a sample of frames are rotated back to a common crystal frame and the FFT search looks for periodicity over thousands of directions; candidate cells are Niggli-reduced, classified by Bravais lattice, refined both constrained and triclinic, and decided on how many validation frames each actually indexes (§4–§7). A failed pass triggers the discrete rescues — the rotation-axis sign, the beam-centre search — before anything is given up on.
First integration pass. At the geometry in the file, every frame is predicted (§8) and profile-fit integrated (§9); partials are combined into fulls, scaled and merged (§10).
Geometry post-refinement. From those reflections the detector distance, beam centre and the cell scale / rotation axis are refined over all frames at once, each step committed only if it improves a held-out residual (§7.5).
Second pass. The sweep is re-indexed de novo and re-integrated at the refined geometry; this
pass is the canonical output, and a guard compares the two passes and keeps the better one
(reported as PASS= / PASS_DECISION= in the report).
Space group. On the P1 merge of the final pass, the point group is scored operator by operator
on resolution-normalised intensities and the screw axes and centring are read from the systematic
absences (§13.1); twinning is checked beside it
(§13.2). CANNOT_DETERMINE and an enantiomorphic pair are real
answers here, not evasions.
Scale and merge. In the determined group: per-frame scales, the cross-validated correction surfaces (decay, absorption, modulation), the error model and ISa, outlier rejection, the CC½-based resolution cut, the anisotropy description, French–Wilson amplitudes and the R-free flags (§10, §13.3–§13.5).
Write. The merged .mtz / .cif / .hkl, the unmerged MTZ, the P1 cross-check and the
results report land next to each other (Output files); with
--model, validation runs first and the maps and the placed model are written too
(§14).
Stills instead. Serial data skip the two-pass machinery: each image is indexed independently
(with the known-cell ffbidx indexer where a cell is given), partiality comes from a per-crystal
orientation-tilt post-refinement rather than a rocking curve, and a merohedral indexing ambiguity
has to be broken per image, at integration time, against a reference or a model
(Advanced ▸ the indexing ambiguity).