Symmetry operators were scored by Pearson correlation on raw merged
intensities. Both members of a symmetry pair sit at the same |s|, so the
resolution fall-off is variance the two arms share exactly, and it inflates
the correlation of true and false operators alike.
The clearest demonstration is the test this commit adds: a synthetic data set
with no symmetry at all - a radial fall-off times an independent per-
reflection factor - is assigned point group 432 by the shipped code, with all
23 rotations confirmed at 0.632 to 0.656. The existing suite passes
identically before and after, because nothing covered this. The new case
fails 64 of its 100 assertions on the old scoring and passes on the new.
On real data the same effect had the gate leaking: on one cubic crystal three
pseudo-symmetric operators scored 0.506 to 0.517, above the 0.5 bound, so
they were confirmed and 432 had to be refused further downstream by the
twin-law and systematic-b guards. Scored on E-squared they read 0.283 to
0.298 and exactly the eleven genuine rotations of 23 are confirmed.
The normalisation has to be over the reflections the correlation actually
pairs. Reusing the existing normalised array is worse than doing nothing: it
is normalised over the set the absence tests use, whose surviving fraction is
itself resolution-dependent, and the coupling to the resolution cut rises
from 0.086 to 0.262 against a raw baseline of 0.086. Normalised over the
paired set it falls to 0.023.
The twin-law H statistic keeps its own vectors on raw intensities. It shares
the pair arrays with the correlation, and normalising in place moves it by up
to 12% against a bound whose window is 5.5% wide. Verified rather than
assumed: two instrumented binaries print the same H to twelve significant
figures while the correlation differs.
min_operator_cc goes 0.5 to 0.30. Normalised correlations run lower, and the
observed window on rugnux's own search merges is 0.298 to 0.351; 0.35 is too
high, because one crystal's weakest genuine operator reads 0.351. The
headroom between a crystal's weakest true operator and its own measured false
-operator floor widens on 14 of 14 crystals, median 0.430 to 0.619, and the
worst operational margin goes from 0.031 to 0.051.
Battery, twice, against a baseline reproducible to zero: the space group is
identical on all 38 crystals, per-shell merging is 0 better and 0 worse
across all 380 shells, and the merged mmCIF is byte-identical on 38 of 38 -
on the 12 crystals whose integration radius now adapts as well as the 25 that
do not. The arm is live rather than inert: all 313 operator correlations move
while every pair count and every H value stays bit-identical, and on one
cubic crystal three operators that raw intensities confirmed are rejected,
with the space group unchanged.
Following Padilla and Yeates (2003) Acta Cryst. D59, 1124-1130 for why a
resolution-normalised statistic is the right one for a symmetry test.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P
leonarski_fandClaude Opus 5
f6bfa54624
