Supercell probe, log-only part: the class it reads over 20-3 A is followed out to the run's own
limit (a second prediction of the same supercell on the same 60 frames, so the 20-3 A band and the
SUPERCELL_* keys are unchanged). Half-integer reflections are counted only where no lattice
reflection predicted on the same frame lies within r3, and each resolution shell is read against the
median of the six other parity classes - which a single doubling leaves empty - as an excess in units
of the lattice's intensity and as a z in the class's own standard errors, the strongest sibling's z
beside it ("Supercell probe to the limit" in the log).
Doubled-cell hypothesis: where that class stands clear of the six empty ones (measured above its
noise and at more than twice the strongest of them, in at least three shells), the run integrates and
merges the doubled cell too, forcing the last pass's indexing result with its lattice doubled along
the class (orientation, geometry and axis kept). One of the two is written as the answer, the other's
merged .mtz/.cif/.hkl beside it as <prefix>_doubled or <prefix>_halfcell; the report names both
(DOUBLED_CELL_*). Which one is the answer is a policy behind one constant: ADDED_CLASS_SIGNIFICANT
(the doubled cell wherever the class stands clear) or HALF_CELL_BREAKS_DOWN (default: only where the
class reaches a quarter of the lattice's intensity in the finest shell both are measured in).
The doubled lattice is classed with a near-zero tolerance: the default lattice search promoted a
triclinic doubled cell with an 88.2 deg angle to orthorhombic C, and no frame indexed.
Measured on forced doubled-cell merges (rc175 b530c2d base): the open-arm crystal deposited in the
doubled cell merges at R-free 0.275 against its deposited model, against 0.574 in the half cell
(odd/even 0.02 at >8 A rising to 0.65 at 1.95 A, odd half-set CC1/2 0.93 at 8-5 A). Five crystals
deposited in the half cell read classes the doubled merge holds as well (odd CC1/2 0.73-0.98 at
8-4 A): two rise with resolution like the first (to 0.4-0.5 at 2.5 A), one is strong from low
resolution (0.3-0.5), two stay flat at 0.1-0.2. Nothing measured on intensities - the trend, the
neighbour correlation, the separation from the nearest lattice reflection after the r3 filter -
separated the doubled deposition from the rising half-cell ones, so the policy is the owner's call.
Also: the SUPERCELL_POSSIBLE prose no longer says correct cells "read the same", and the warning no
longer advises -C with the doubled cell, which the indexer reduces back to the half cell.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SVmAWnzCmRKAXVUCdc4iNi
leonarski_fandClaude Opus 5.5
55dd0d4f6b
