leonarski_f
07ae590e54
Where the space group is given (-S) and its lattice admits alternative indexings, a stills run without -z or --model used to merge the crystals' random indexings together (and warned). The crystals are now made consistent with each other before anything is scaled (ReferenceFreeReindex): each takes the indexing in which it agrees best with all the others (Brehm & Diederichs 2014), agreement being the sum over shared reflections of the products of shell-normalised, per-crystal standardised intensities, weighted by 1/(1+(sigma/sd)^2). The sum over all pairs is (|M|^2 - const)/2 for M the running sum, so a pass over the crystals is one pass over the reflections rather than over all pairs: coordinate ascent, four seeded starts, stop when <= 1 crystal in 1000 moves, the overall relabel that moves the fewest crystals. Deterministic (fixed summation order, sequential passes). A twin law of a pseudo-merohedral cell whose axes differ by a few per cent is decided by the crystals' own refined cells, which the indexer has already used: where >= 90% of the crystals' cells fit better as indexed, those crystals are anchors and only the others are decided by the intensities. Without this, two public sets got worse (pal90 R-free 0.183 -> 0.207, lcls242_t 0.296 -> 0.350). With a reference or model the per-image choice stands; the same resolution runs as a check, reported as AMBIGUITY_DATA_DISAGREES. New report keys (section 2): INDEXING_AMBIGUITY_RESOLVED, AMBIGUITY_CRYSTALS, AMBIGUITY_REINDEXED, AMBIGUITY_SEPARATION_SIGMA, AMBIGUITY_DECIDED_FRACTION (+ AMBIGUITY_TIME_S, dev). --mode scale is not changed. Still battery, no --model (R-free, REFMAC 0-cycle against the deposited model; before -> after; with --model for comparison): euxfel83 0.321 -> 0.207 (0.204), euxfel152 0.346 -> 0.257 (0.245), alvra213 0.209 -> 0.201 (0.207), alvra213_int16 0.210 -> 0.202 (0.208), pal90 0.183 -> 0.183 (0.188), lcls242_t 0.296 -> 0.294 (0.285); controls sacla237 / lcls222 unchanged (no ambiguity, no-op). The step takes 0.2-1.6 s on 2.7k-54k crystals; synthetic 64k crystals x 200 reflections 0.5 s. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 80d378a1fe92364fd5b99a17f5c9ee8498412d36)
Jungfraujoch
Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with
rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular
and small-molecule - from images to merged reflections.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.