A change that touches partiality - a mosaicity estimator, a rocking-curve
model, a background change - cannot be judged by the statistics we normally
reach for, and this was learned the expensive way. ISa is anti-correlated with
external accuracy and is the largest mover of any statistic; last-shell R_meas
moves with its denominator, i.e. the wrong way by construction; `--model`
R-free tracks its own zero-information floor, which shifts ~22x more than
R-free itself over the same sweep; and per-shell agreement with XDS is biased,
because XDS never divides by partiality, so "divide less" moves us toward it
mechanically - measured to put the optimum ~1.4x too low.
Anomalous difference density at known scatterer sites has none of those
problems. It is read in units of the map's own sigma, so the uniform intensity
rescale a partiality change produces cancels exactly, and it is referenced to
the structure rather than to another program's partiality model.
The script runs SHELXC + ANODE per arm against a model placed ONCE and then held
fixed, and reports the mean site height, the off-site noise floor, and the
paired per-site change between arms. Numeric arm labels turn a set of arms into
a curve with a per-dataset optimum. The dataset table lives outside the
repository, as rugnux_vs_xds.py already does for the battery, because dataset
and sample identities are not committed.
It reproduces the measurements it was built from: all nine points of three
pooled curves, every per-crystal optimum, the site heights, the paired t
statistics, and the adversarial control in which a model refined against the
worst arm reproduces the curves to <=0.005 and the same optimum on 4/4.
Four things the ad-hoc scripts it replaces got wrong, all now handled:
* Keying sites on the ANODE atom label silently drops an alternate conformation
sharing that label - one dataset class has 18 sulfur sites, not 17, and the
uncorrected mean read 15.03 against a true 14.49.
* The off-site floor skipped any peak within 1.0 A of ANY atom, so a ripple
sitting on a light atom was not counted as background; requiring 1.5 A from an
anomalous scatterer raises one floor from 7.12 to 9.48 sigma.
* Special-position peaks are Fourier ripples, not background. Excluding them is
load-bearing on 3 of 9 datasets and they are now reported in their own column
rather than dropped silently.
* Enantiomorph care turned out to be unnecessary - passing the merged file's
screw label to ANODE while the model sits in the other hand gives byte
identical peaks. What does matter is the pair whose absences are identical,
I23 vs I2_13, which phaser's automatic hand test does not cover.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
rugnux gained --model - R-free and 2Fo-Fc/Fo-Fc maps against an atomic model, and with it
the resolution of the enantiomorph and of a merohedral indexing ambiguity - without the
page ever mentioning it. It was the only option missing; the two lists now agree in both
directions, checked against the usage the binary prints.
The viewer page still said results are never saved and that no Windows package exists.
Both have been false for a while: the Processing panel runs full rugnux jobs on the open
dataset, writes _process.h5 and the merged reflections, registers each run as a
selectable view so runs can be compared, and can hand out the equivalent command line for
a cluster; and the installer is published with every release. The mask menu also loads
TIFFs now, and the View menu has layout presets.
The writer page documented -R for the root directory, which is the back-compatibility
alias for -d, and an HTTP status interface that no longer exists - status reaches the
broker over the writer notification socket, and a writer is stopped with a signal.
The test page pointed at .gitlab-ci.yml and at jfjoch_offline_process, which is not a
binary any more; the CrystFEL fixture pointed at HDF5DatasetWriteTest, which is not
either. The broker page linked ../broker/redoc-static.html, which MyST resolved by
copying the 700 kB file into _downloads/ rather than using the copy already in _static.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5