leonarski_fandClaude Opus 5
e576184e2f
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The rugnux page opened with installation and reached its quick start around line 500 of 840, which is not where someone who wants to process a dataset looks. It now opens with four commands - the defaults, a reference MTZ, a model, and a pinned cell and space group, which is what people actually ask for - followed by the five files a run leaves and a few pointers. The old quick start keeps the detailed walkthrough under "Running rugnux", moved up to sit after the orientation sections. The indexing ambiguity had no prose anywhere, and neither did -z, which had one row of a table for four different jobs. A new section says what a reference MTZ does, what the ambiguity is, that it costs a rotation run an arbitrary frame and a serial run its CC1/2 outright, how to resolve it in each of the four cases, and that it is neither the enantiomorph nor twinning - the two things it is most often taken for. The three long reference pages carry a table of contents, from the MyST contents directive rather than a hand-written list, so it cannot go stale. The theme's sidebar already lists each page's H2 headings, so this adds the level below that and an in-page map; splitting the pages was the alternative and would have broken every anchor other documents link to. Two things the code says that the docs did not. --mode scale does not accept a reference MTZ on rotation data - the rotation scaler refuses it and the run stops - where the page offered it as one of the things to re-merge with. And CPU_DATA_ANALYSIS 10.9 still said stills use the reference as their per-image scale target, which stopped being true when stills were changed to scale against their own merge; the reference is their per-image ambiguity test and nothing else. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Vi1gV6Z45aZL5wLwe85Ksn
Jungfraujoch
Application to receive data from the PSI JUNGFRAU and EIGER detectors.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.