The final stills merge drops every crystal whose cell is not close to the consensus cell
(MergeOnTheFly::Mask), but the scaling reference (MergeAll) and the partiality post-refinement
were made over all of them. On two 25k-frame XFEL runs of a tetragonal crystal those were 26-30%
of the indexed frames and 60% of the integrated reflections: weak frames (median 8 indexed
spots) indexed in a 2x/3x/4x supercell or an unrelated lattice, whose supercell-only reflections
are pure noise and whose indices do not name the true reflections. They went into the
reference every merged crystal was scaled against, and through the tilt refinement.
MergeAll and StillsPartialityRefine::Run now take the reference cell and use only the crystals
it accepts - the same test, with the same tolerances, as the merge.
Measured (both runs, mx path): CC1/2 0.9599 -> 0.9598 and 0.9645 -> 0.9644, I/sigma +0.05 and
+0.02, R_pim unchanged, space group and resolution unchanged; --mode scale against a deposited
tetragonal lysozyme model CC 0.9452 -> 0.9477 and 0.9461 -> 0.9473. Scale+merge 2.1x faster on
--mode scale (14.6 -> 6.9 s, loaded box).
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 5.5
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