leonarski_fandClaude Opus 5
f2b92e3f4d
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zeta is the sine of the angle between a reflection's rocking path and the spindle. Near 0 the reflection crosses the Ewald sphere almost tangentially, spends many frames in diffracting position and is measured worst. The de-novo space-group search asks how EQUAL an operator's paired intensities are, so its answer is dominated by whichever reflections are measured worst - and when the spindle lies in a lattice plane, an operator that permutes the two in-plane axes samples a different mixture of measurement qualities than one that only flips signs. That is not a fair comparison, and it can make a real symmetry operator look like a twin law. Measured on a thaumatin set mounted that way (its 4-fold is 88.9 deg from the spindle), the added operators' disagreement is 1.74x the parent's over pairs where both reflections have zeta < 0.85 and 1.003x - i.e. the symmetry is exact - over pairs where both are above it. The search consequently refuses the 422 promotion and merges the crystal in P222, while the same data forced to the right group give CC1/2 99.2% at multiplicity 10.7, matching XDS. With the option the de-novo pass ignores those observations (the final merge keeps everything - there completeness is the point): zeta cut observations ignored H ratio adopted 0 (off) - 1.47 P222 0.5 1620648 1.44 P222 0.7 3006013 1.34 P21212 0.85 4536724 promoted P4212 (correct point group) OFF BY DEFAULT, and it must stay off, because the same cut costs four other crystals their space group (P41212 -> P212121, I23 -> P2, I23 -> I222 twice): at 0.85 it discards 40-80% of all observations, which on a crystal whose geometry is not the problem simply starves the search. Two independent implementations - filtering the pairs that enter the statistic, and filtering the observations that enter the merge - trade exactly the same crystals, so this is a property of the cut and not of where it is applied. Verified bit-identical to the previous binary when off. The companion diagnostic is already there: the run now reports how close a symmetry axis lies to the spindle, which is the geometry that makes this option worth reaching for. Implementation note for anyone tempted by the cheaper route: excluding these observations from the ASU grouping alone does NOT work. The 3D combine selects partials on corr, not on their group, so their intensity still reaches the fulls and the merged intensities are unchanged - measured, the statistic did not move by 0.03 while 67% of observations were nominally excluded. Zeroing corr is what removes an observation from the combine, the merge and the error model alike. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>