"Analyze dataset" and `rugnux` with no options are two front ends onto the same
library and are meant to agree, but they decided their defaults separately and
the two lists had drifted. The viewer was missing:
- the de-novo starting point. The CLI discards the cell and space group stored
in the input file before it does anything; the viewer left them on the
experiment. Rugnux only searches for a space group when none is set, so the
search was skipped entirely and the stored group was reported straight back.
That is self-reinforcing: a finished job's own _process.h5 becomes the active
snapshot, so a run that ended in P1 pinned every later run to P1 - which is
what "lysozyme keeps coming out P1 in the viewer" was.
- the polarization factor, so the Lp correction was omitted altogether. The
missing factor is azimuthal and intensity-proportional, and symmetry mates sit
at the same 2-theta but different azimuth - the exact "unequal intensities
forced together" signature the space-group search vetoes as pseudo-symmetry,
which can land a genuinely de-novo run in P1 on its own.
- five rotation scaling defaults: the smooth-G range, the minimum captured
fraction, the capture-aware sigma, outlier rejection and --search-min-zeta.
The CLI's own comments tie the captured-fraction default to a crystal
recovering its true space group instead of P1.
Put the policy in one place (RugnuxDefaults) and have both front ends start from
it. The CLI now takes its defaults from there and applies user options on top;
its output is unchanged, verified bit-for-bit on four battery crystals.
The stored cell/group is still available: the job dialog offers "Use the stored
unit cell / space group", off by default, shown only when the file has one.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5
e8a7696ffe