With -S the prediction rejected the fixed group's centring absences, so those reflections were never
integrated. Two things followed, and only the second was known.
The P1 cross-check was withheld on such a run, because a P1 merge missing whole centring classes is
misleading rather than merely small - 50% of the nodes on an I lattice, 75% on F, 67% on R. That was
the documented reason and it was right.
The unknown one is that it cost intensity accuracy. Every predicted reflection marks its signal region
so a neighbour's background ring can exclude it (BraggIntegrationEngineCPU, the reflection mask); an
unpredicted node is an unclaimed patch of detector, and the neighbouring reflections sweep those pixels
into their background and over-subtract - worst at high angle, where the background dominates. On a
fixed F-centred group that is three quarters of the nodes: measured against the de-novo run of the same
data, <I/sigma> 16.07 against 17.21, CC1/2 0.9862 against 0.9895, ISa 10.93 against 11.92.
Predicting them costs nothing downstream, because both merges already decide absence against the group
they are merging in: the run's own merge drops them again, and the P1 cross-check keeps them because P1
has none. One integration, two correct merges. The -S output becomes byte-identical to the de-novo run
on the five crystals measured, which is the point - pinning a group should not change the answer - and
such a run can never be slower than de novo, since it predicts the same reflections and additionally
skips the space-group search.
The de-novo path is untouched by construction: it already predicted in P.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
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