The beam-centre check indexes a second first pass at the measured centre and,
where the two centres return cells related by an integer volume factor, says so
and decides nothing. That abstention is right in general - the validation frame
count leans to the sub-cell, since a cell twice as long must place every spot
twice as accurately to score the same - but it leaves one direction
unrecoverable. Where the MEASURED centre holds the LARGER cell, the run starts
on the sub-cell and stays there: the second pass re-finds the larger cell at the
refined geometry and its supercell guard refuses it for being larger than
pass 1's. The run then merges a halved axis at full indexing rate, with good
merging statistics and nothing to say it is wrong.
Decide that one direction, on the pooled spots rather than on the frames: the
excess each lattice puts on itself over its own wrong-spindle null, which is the
measurement the failed-pass branch of the same check already adopts a centre on,
and the one statistic that does not credit a denser lattice for accidental hits.
The opposite direction is deliberately left alone - a second pass is free to drop
to the smaller cell and does, on every corpus crystal that reaches this branch
that way.
Measured on a tetragonal crystal whose header centre is 3.6 px out across the
spindle, more than the geometry absorbs: the file's centre gives a halved a axis
(43/60 frames, 25.4% of the pooled spots on the lattice) and the measured one the
deposited cell (60/60, 43.3%). Before, the run merged the halved cell and the
deposited model refined to R-free 0.575; after, it merges the deposited lattice
to 1.62 A with R-free 0.254 against the deposition's 0.203.
Five other corpus crystals reach the same branch with the measured centre on the
SMALLER cell; all five are unchanged (space group, cell and R-free identical), as
are two crystals whose halved or doubled axis comes from elsewhere.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_013nW6FNRP1bBJJ8pfHiByAT
leonarski_fandClaude Opus 5
df4be47c84
