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* 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>
53 lines
2.6 KiB
Markdown
53 lines
2.6 KiB
Markdown
# Download the Jungfraujoch Viewer
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`jfjoch_viewer` is a standalone desktop application, pre-built for Linux, macOS and Windows with
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the Qt runtime included. The links point at the current release; the full list of what each release
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ships is on its release page.
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```{eval-rst}
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.. jfjoch-downloads:: viewer
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```
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On a machine with an NVIDIA GPU take the **GPU** build: its embedded spot finding, indexing and
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integration run on the card, and it also starts on a machine without one, on the CPU. The **CPU
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only** build runs the same pipeline at lower throughput and is the smaller download. A V100 needs
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the CUDA 12 build; the CUDA 13 builds start at Turing (T4) — see
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[Release contents](RELEASE_CONTENTS.md#gpu-generations-and-the-nvidia-driver).
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## After downloading
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**Linux.** The archive has no top-level directory, so unpack it into a directory of its own, then
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run the program from its `bin/`:
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```
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mkdir -p ~/jfjoch_viewer
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tar xzf jfjoch_viewer-<version>-linux-cuda12.tgz -C ~/jfjoch_viewer
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~/jfjoch_viewer/bin/jfjoch_viewer dataset_master.h5
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```
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The archive also carries the desktop entry, icon and D-Bus service file under `share/`, which the
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desktop picks up when the archive is unpacked into a prefix it searches, such as `/usr/local`. The
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Linux repositories carry the viewer as the `jfjoch-viewer` package as well
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([package repositories](REPOSITORIES.md)).
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**macOS.** Open the disk image and drag `jfjoch_viewer` onto the *Applications* shortcut next to
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it. The image is signed and notarized by Apple, so it opens like any other application. Apple
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Silicon only; Intel Macs are not supported.
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**Windows.** Run the installer. The CUDA and CPU variants share one install directory and replace
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each other, and are told apart in *Add/Remove Programs* as *Jungfraujoch (CUDA)* and *Jungfraujoch
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(CPU)*.
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Then **File ▸ Open** a Jungfraujoch or NXmx master file, a `_process.h5` written by Rugnux, or any
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frame of a miniCBF, marCCD or SMV sweep; **File ▸ Open HTTP** follows a live collection from a
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running broker. [jfjoch_viewer](JFJOCH_VIEWER.md) is the manual, with a
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[guided tour](JFJOCH_VIEWER.md#a-guided-tour) of the four views most people use.
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## From source
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The viewer builds on Linux, Windows (MSVC and CUDA) and macOS; Qt 6 is the one dependency that
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has to be installed first, everything else is fetched by the configure. See
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[Building from source on Windows](JFJOCH_VIEWER.md#building-from-source-on-windows) and
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[on macOS](JFJOCH_VIEWER.md#building-from-source-on-macos); on Linux configure the full tree with
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`-DJFJOCH_VIEWER_BUILD=ON` ([Deployment](DEPLOYMENT.md#install-jungfraujoch-image-viewer)).
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