A crystal of slightly misaligned domains (a ferroelastic domain twin below a phase transition, a
split crystal) records each reflection as two or more compact spots around the averaged lattice's
prediction, moving apart with resolution. The pre-scan footprint is measured about each spot, so it
saw compact spots; the r1 disk held the gap between them and the background ring sat on them.
The geometry pre-pass now compares every indexed spot with the predicted position of its own
reflection on the same frame and adds the mean square offset (radial and tangential, by distance
from the beam) to the pre-scan widths; the canonical pass integrates with that table. Where spots sit
on their predictions this moves the widths by the prediction error alone (lysozyme: 0.2-1.0 px, no
reflection outgrows r1); on a 100 K KDP domain twin the offsets reach 8-16 px at the edge.
KDP (kdp_x10sa_20keV), battery SHELXL recipe on the COD model: R1 0.272 -> 0.048, wR2 0.685 ->
0.129, EXTI 26.9 -> 0.025, GooF 3.2 -> 1.29 (XDS: 0.112 / 0.333 / 0.054 / 1.25); R_meas 21.6% -> 5.3%.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB
The integrator's r1 disk and r2..r3 background ring are fixed in pixels and chosen from spots near
the beam. On small-molecule data at 20-25 keV a spot's standard deviation grows from ~1 px near the
beam to ~5 px at the edge (radially from parallax/obliquity, tangentially from the crystal's
azimuthal spread), so the r1 = 4 disk holds a quarter of the flux there, the background ring a third
of it, and the in-disk second moments the Gaussian is built from saturate near r1^2/4. On top of
that, the profile/summation runaway guard sent 20-30% of these reflections - the strong, wide ones -
back to the truncated r1 box sum.
- SpotFootprint: every pre-scan spot (width frames) is measured with a window that follows it
(3 sigma, iterated, re-centred), radially and tangentially; the medians per distance-from-beam bin
become BraggIntegrationSettings::Footprint. Installed only where some bin outgrows r1, and on the
adaptive side like the radius (pre-pass without; the starvation guard falls back to the settings
without it).
- BraggStencil: where 3 sigma > r1 the background ring starts at 3 sigma along and across the radius,
the summation region is the r1 disk plus the 3-sigma footprint ellipse (so the guard's fallback is a
complete intensity), and the per-reflection Gaussian takes the footprint widths. Compact spots keep
the stencil bit for bit. Both engines build it from the same header.
SHELXL against COD (R1 / fixed-XDS-model R1(F)): citric acid .101/.230 -> .077/.055, HEPES
.070/.179 -> .048/.050, aspirin 20 keV .059/.070 -> .052/.061, aspirin 25 keV unchanged, L-cystine
25 keV unchanged (.145 -> .144).
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB
leonarski_fandClaude Opus 5.5