leonarski_f
63f5f96132
* Rugnux: A placed model is refined by default - restrained maximum-likelihood refinement on the GPU (CPU without one), writing `<prefix>_refined_model.cif`, `<prefix>_refined_maps.mtz` and the difference-map blobs in `<prefix>_blobs.json`; `--no-refine` skips it. * Rugnux: `--mode refine` refines a model against merged structure factors from an MTZ or mmCIF file. * Rugnux: The embedded restraint dictionary covers amino acids, nucleotides including common modified RNA nucleotides, common cofactors, crystallisation additives, waters and ions, with metal sites restrained from the model's LINK records. * Rugnux: A model or reference file can be given among the inputs in any order, recognised by its contents. * Rugnux: The geometry refinement algorithm option is now `-r, --geom-refine` (was `--refine`). * Rugnux: Serial stills resolve the indexing ambiguity from the data when no model or reference is given, reject merge outliers by default, follow the run's measured rocking curve in prediction and partiality (also in `--mode scale`), and index reproducibly on the GPU. * Rugnux: Reflections touching the beam-stop shadow are not integrated, reflections coarser than the low-resolution limit are merged and written (but kept out of the scale fit), and the polarisation plane is measured more reliably. * Rugnux: Small-molecule runs report unit-cell e.s.d.s, in a SHELX `.ins` beside the `.hkl` and in the mmCIF. * jfjoch_broker: Live Rugnux refines the uploaded model after placement; the web frontend's Rugnux live page has a hero panel with resolution, ISa, space group, placement and refined R-work/R-free, and its Mol* viewer shows the refined model and maps. * Documentation: A new front page with download pages for Rugnux and the viewer, and the technical reference reorganised below it. * Build: The fast-feedback indexer is part of the source tree instead of being downloaded at build time. Reviewed-on: #91 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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Naming
The software is Swiss, and so are its names: both halves of the system are named after places in the Alps that are, in one way or another, about moving a lot of something up a steep mountain as efficiently as possible — usually by train. Throughput, in other words.
| Part | Name | What it does |
|---|---|---|
| Streaming / acquisition | Jungfraujoch | Receives detector data at high data rates, runs the FPGA/GPU pipeline, and streams images out for writing. |
| Data processing | Rugnux | Crystallographic analysis of a stored dataset, or of a collection while it is written — indexing, integration, scaling and merging, and refinement of a given model (the rugnux tool). |
Jungfraujoch
The Jungfraujoch is a high mountain col in the Bernese Alps, the saddle (Joch is German for "yoke" or "col") between the peaks Jungfrau and Mönch, at 3,466 m. It is the site of the High Altitude Research Station Jungfraujoch, whose long-running atmospheric measurements are co-operated by the Paul Scherrer Institute — the same institute that develops this software and the JUNGFRAU detector.
The name is also a small piece of word-play. PSI's JUNGFRAU detector and DECTRIS's EIGER detector are both named after Bernese Alps peaks (the famous trio is Eiger, Mönch, Jungfrau). The Jungfraujoch — the pass between Jungfrau and Mönch — is where those two detector worlds meet.
And it fits the theme of the whole project: the Jungfraujoch is reached by the Jungfraubahn, whose terminus is the highest railway station in Europe (3,454 m, the "Top of Europe"). It is the closest you can get to that summit in a genuinely high-throughput way — by train, moving crowds up the mountain — which is exactly what the streaming side of this software does with detector frames.
Pronunciation (German): Jungfraujoch ≈ YUNG-frow-yokh. "Jung" as in young, "frau" rhymes with cow, and the final "joch" ends in the guttural ch of Scottish loch or German Bach — not a hard k.
Rugnux
Piz Rugnux is a mountain in the Rhaetian Alps of canton Graubünden, in south-eastern Switzerland. (Piz is the Romansh word for "peak".) It rises above the Albula line of the Rhaetian Railway (Rhätische Bahn), part of the "Rhaetian Railway in the Albula / Bernina Landscapes" — a UNESCO World Heritage Site (Welterbe).
That stretch of line is a masterpiece of throughput engineering: to climb a great deal of altitude in very little horizontal distance, it corkscrews through a series of helical (spiral) tunnels looping back inside the mountains. It is, again, the Swiss art of getting an enormous amount up a steep mountain efficiently — the same idea the data-processing side of this software is built around: pushing a large volume of diffraction data through the analysis pipeline.
So the theme is consistent — Swiss mountains, trains, and throughput — while keeping the two subsystems clearly distinct: Jungfraujoch streams, Rugnux processes.
Pronunciation (Romansh): Piz Rugnux ≈ peets roo-NYOOKS. The "gn" is a soft palatal ñ, as in canyon or Italian gnocchi, not two separate sounds.
What is Romansh?
Romansh (Rumantsch) is the fourth national language of Switzerland, alongside German, French and Italian. It is a Romance language — a direct descendant of the spoken Latin left behind in the Alpine valleys — today spoken by only a few tens of thousands of people, almost all in the canton of Graubünden. It survives in several regional idioms, brought together in a standard form called Rumantsch Grischun. Naming the processing engine with a Romansh mountain is a small nod to the least-spoken but no-less-Swiss corner of the country.