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leonarski_fandClaude Opus 5.5 baf2017c97 Defective pixels: mask a persistent patch, not only a lone pixel; sub-lattice ask reads the R contrast

Two defects that together turned a tetragonal small-molecule crystal (open-arm cuhf2, published
P4/nmm) into P222.

1. HotPixelFinder masked a persistent strong pixel only when it stood alone or in a pair ("a
   larger patch is a feature of the scattering"). On cuhf2 a ring of ~20 pixels reads 1e5-3e5
   counts on EVERY frame (dead centre) - stationary in the lab, so no reflection of the rotating
   crystal. Unmasked, the reflections crossing it ((2,6,+-9)) merged to 3.5e6 / 6.7e5 against 4e4
   for the strongest real reflection. The final merge's outlier test removes them (12
   equivalents), but the space-group search's P1-like merge has no equivalents to judge by, and
   the h<->k operator read CC 0.18 / R 0.28 instead of ~0.99 / 0.013. The persistence and strength
   tests are unchanged; only the isolation requirement is dropped.

2. The sub-lattice ask kept every metric two-fold that passes min_operator_cc. On a pseudo-cubic
   cell two false cubic two-folds still correlate at 0.31-0.33, LePage closes them with the
   genuine ones into the full cubic metric, and the tetragonal class in between is never asked.
   An operator now also has to pass the R contrast every promotion's added operators are held to
   (min_operator_r_contrast against random_pairing_r / global_best_operator_r, read only where the
   search reads it): the false ones sit at 0.2, the genuine ones at 1.0.

cuhf2: P222 -> P422, R_meas 2.9% -> 2.6%, ISa 45.5 -> 52.3 (overnight-cint had found P422 by the
sub-lattice path; rc174-all lost it). Prescan survey, masked pixels base -> new: unchanged on
lyso_x06da_ref/5keV/atten_wedge, thau, insu, cytc, myob_split, 9qw8, aspirin20, HEPES, YAG,
metformin, nidppe; cuhf2 3 -> 42, 5reo 2 -> 6, lcystine25 0 -> 9 (two clusters of noisy pixels at
3-7 counts/frame on a zero background). Targeted battery (sm2rest-fix vs rc174all-ctl / smt-all):
the 15 protein / sub-lattice sets (lyso x3, thau, insu, cytc, myob_split, 5reo, 9qw8, 6iu6, 6iu8,
6iu9, 6z8o, 8t7r, 9ea5) identical to the 4th digit; SM sets identical except cuhf2 (above) and
lcystine25, SHELXL R1 .112 -> .151: the nine masked pixels flip the fulls-only per-frame scale
smoother on that polycrystalline sweep from "settled after 29 iterations" to "stopped settling"
(the base run reproduces bit-identically) - a sensitivity of that smoother, reported to the
scaling work, not of the mask.

Test: HotPixelFinder_PersistentPixelNotBragg gains a 3x3 patch that must be masked. The
device-vs-host test now waits for each queued frame before overwriting the shared device buffer;
it remains flaky at ~4/25 on the base binary as well (a borderline pixel or two differ), which is
pre-existing and not addressed here.

Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB

2026-10-04 20:42:11 +02:00