2 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	7eed4a5e0b	Battery: SHELXL refinement of each small molecule's COD structure, reported per run ... shelx_check.py refines the row's published structure (manifest key "cod", cached from the Crystallography Open Database into the site's cod_cache) against rugnux's p.hkl with one fixed recipe: data reindexed into the COD setting (lowest-R1 integer matrix), non-H anisotropic, H fixed, EXTI, MERG 2, three rounds of SHELXL's suggested weights. It records R1/wR2/GooF/EXTI/WGHT/residual density/R(int)/R(sigma)/K of the strongest bin and a fixed-model R1(F) (|Fc| of the COD model as published, gemmi). Reported, never scored. The report gets a small-molecule table; compare lists SHELXL R1/wR2/GooF/EXTI deltas; report/compare fill the check in for older runs. COD entries matched by Niggli-reduced cell and space group: aspirin 7050897, citric acid 5000063, HEPES 2224210, YAG 2003066, L-cystine 1513328 (2005, replaces the 1959 model for refinement), cytidine 2001311, 3,5-dinitrobenzoic acid 4510615, L-alanine 2104782, metformin HCl 2108029, NiCl2(dppe) 2012031. cuhf2 has no reference cell and no match: left without one. SHELXL is called, not shipped (site key "shelxl" or PATH; it comes with CCP4). Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01K5K8jvPPbmCrbqnWkddTuB	2026-10-04 00:57:06 +02:00
leonarski_f	6dfe065365	v1.0.0-rc.172 (#82) ... * Fixed `jfjoch_broker` cancelling every data collection with a CUDA "out of memory" error after long operation: GPU memory no longer leaks with each collection. * Rugnux scales a rotation sweep until the per-frame scales settle instead of for a fixed three rounds, and says so when they did not - merged intensities, and the space group, resolution cut and frame rejection read off them, change accordingly; `--scaling-iterations` is now the cap on that loop (default 100). * Rugnux places every frame of a marCCD, SMV or miniCBF series at the spindle angle its own header states, so a series with missing frames, or with angles written modulo 360, is no longer read at the wrong geometry or refused. * Every rotation run writes two diagnostic files beside its reflections: `<prefix>_detector.jpg`, the detector projection with the pixel mask and the detected beam-stop shadow drawn on it, and `<prefix>_plot.txt`, one row per image. Reviewed-on: #82 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-22 06:48:37 +02:00