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