A pseudo-translation makes one class of reflections systematically strong and the
complementary class weak. It is the classic predictor of a failed molecular
replacement, it raises the second moment where twinning lowers it so each masks the
other's test, and rugnux did not look for it at all.
Look for it: a native Patterson from the merged intensities, the largest off-origin
peak taken as a fraction of the origin, and the vector refined against the data.
Both halves are scored against a null computed for that crystal rather than a bound
taken from elsewhere - the peak against intensities permuted within resolution
shells, the modulation depth against the same search started from random vectors -
because the noise floor of the first runs from 1.35 to 17.7 per cent across the
corpus, so no fixed threshold could mean the same thing twice. Requiring both is
what keeps the false-positive rate down: either alone calls one crystal in ten.
A translation the data are exactly invariant under is a lattice vector, not a
pseudo-symmetry. Recognising that removes eleven false calls from ninety-five merges
folded in P1 - each reading 83 to 102 per cent of origin against a genuine maximum of
62 - and adds one true positive whose pseudo-translation lies underneath its own
centring and is unreachable without it.
Report-only: it gates nothing and changes no reflection, no scale and no group. It
fires on eight of a hundred and thirty-seven crystals, and on those the verdict moves
from OK to WARNINGS, which is the point of it. Median cost 55 ms, worst 1.9 s on the
largest merge here.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
leonarski_fandClaude Opus 5
a4be5e6cd0
