leonarski_f
2dbb9d5951
Three changes to the stills post-refinement and merge, decided on 0-cycle REFMAC R-free against the deposited models (diff = ours - deposited data, noise ~0.002): - Stills merge only observations whose model partiality is at least 0.5 (RugnuxDefaultScalingSettings; rotation keeps 0.02, and --min-partiality still overrides). Diagnosis on per-observation dumps: the empirical rocking curve has a floor of 5-15 % of its peak out on the tail (mis-oriented crystals), and dividing such observations by a small model p makes them biased, not noisy. Variance terms in (1-p) or (1-p)/p recovered a third of what the cut does; a narrower (correct-looking angular) width or a Lorentzian form was worse. On one set in scale mode the optimum is flat over 0.3-0.6. - The CC adoption gate in RefineOne is gone: it left 25-33 % of crystals at p = 1 next to the refined ones, and collapsed to 3 % on a run whose curve is off-centre. - The run's radial scale of the reciprocal lattice (a wavelength or cell a little off, invisible to spot positions since they fix only lambda d*) is measured from where the curve is centred against d*^2 (MeasureRadialScale, iterated three times) and applied to q in the width measurement and the post-refinement. One run had its curve centred at +2-3e-3 d*^2 (scale -1.6e-3 measured); the others measure below 7e-4. --mode scale on stills now starts where the full pipeline starts: p = 1, the excitation error recomputed from the stored lattice (the window was read as zero before, so no run width was ever measured), and collapsed scales rejected after the refinement. Still battery, the 12 non-float sets, change of diff vs the previous build: -0.0035 mean, 9 better, three within +-0.0006 except one +0.0053 (an edge win becoming a draw); the off-centre run -0.005 here and -0.017 in an earlier run of the same algorithm (that set varies by ~0.01 between runs). Rotation p.hkl byte-identical on three sets. Test StillsPartialityRefine_MeasureRadialScale added. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 0d85e5b975ba863828bd17ebc3b5308e9aa294ce)
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.