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>
leonarski_fandClaude Opus 5
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