The serial-stills merge (MergeOnTheFly::CorrectedSigma) weighted each
observation by 1/sigma^2 using the observation's OWN sigma. Below ~1
photon the Poisson signal part of that sigma correlates with the
observation's up/down fluctuation, so the inverse-variance mean is
biased low: an up-fluctuated observation acquires a larger sigma and is
over-downweighted. The rotation combine (RotationScaleMerge::
process_rawrun) already avoids this by rebuilding the signal variance at
the pooled estimate; the stills path did not.
Decompose each observation's variance into a background/read part (kept
per-observation) and a Poisson signal part, and rebuild the signal part
at the reflection's expected <I>. Bit-identical when an observation sits
at its reflection mean; only weak-shell weights move. Now default on, so
the stills path matches the rotation path;
--no-expected-variance-merge restores the old observed-sigma weighting.
Validated by paired refinement (phenix, 5 free-set seeds, byte-identical
free flags across arms): R-free-neutral on strong lysozyme and lower
R-free on weak serial-stills data checked against an independent
deposited model (6/6 seeds). The CC1/2 dip on strong data reflects
precision, not accuracy. Applies to both offline rugnux and the online
broker stills merge.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
leonarski_fandClaude Opus 4.8
cbc6a85157