leonarski_fandClaude Opus 5
d28db19ab1
A reflection the group predicts absent counted as a violation when
I/sigma > 3 AND E^2 = I/<I>(shell) > 0.3. Neither half survives contact
with real data:
* merged sigma is floored at b|I|, so merged I/sigma saturates at ISa
for nearly every reflection - the I/sigma half is an on/off switch
keyed on ISa vs 3, not a per-reflection test. On one crystal the
absent class read <I/s> 4.10 against 3.73 for the present class while
being genuinely extinct;
* <I>(shell) decays with resolution while a systematically-absent
reflection keeps a small NON-decaying residual (background / profile
leakage), so absent reflections drift over an absolute E^2 cut at high
resolution. That cost a tetragonal 42_12 crystal its 4_1: 18 of its 47
absent 00l crossed the cut, all beyond 3.7 A, at absolute intensities
identical to the low-resolution ones correctly judged absent, while
their l=4n row-mates sat 20-60x higher at the same resolution.
A screw extinguishes only the reflections that lie ON its axis, so the
fair yardstick is the rest of that same row. The threshold is now
0.3 * max(1, median E^2 of the reflection's own row), the row being the
gcd-reduced reciprocal-space direction and the control class the same-row
reflections the group predicts present. Floored at 1, so it only ever
relaxes: a screw can be recovered by it, never lost.
Per row, not pooled. A 4_1 along c and a 2_1 along a are separate
conditions with separate controls; pooling let the weak a/b rows (median
E^2 ~0.5) set the threshold for a strong c row (8.4) and the rescue never
fired.
The candidate table now reports the screw evidence (median E^2 of the
absent class and of its rows) - the <I/s> columns are the centering
evidence and say nothing about screws, for the sigma-floor reason above.
Rotation battery, 33 crystals: 31 decisions bit-identical, the 42_12
crystal recovers its 4_1 (0 violations, row E^2 8.4 vs absent 0.12), and
one crystal with a long axis and heavy 00l overlap moves to a 4_1 group at
exactly 10.0% violations - marginal, and its sister crystal of the same
form sits at 13.3% and does not move. Real screws now span 0-9.3%
violations, so max_absent_violation_fraction cannot be tightened below
0.10 without risking a genuine one.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.