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leonarski_f 1b48f3873f docs: front page and quick start - Rugnux goes on to a refined structure with a model

Landing page (title, hero, lede, Rugnux card), the documentation home's Rugnux card and the opening
of RUGNUX.md now say what the program does: from diffraction images to merged data and, with a
model, on to a refined structure and maps.

RUGNUX.md Quick start is rebuilt around how a run is started: rotation (master file, or the first
frame of a CBF/marCCD/SMV sweep), serial stills (several masters or all of a dataset's files by
glob), serial stills with -C/-S and --crystfel-geometry (wavelength/distance flags only where the
files state neither), and with a model (positional or --model): placement by rigid body or MR,
refinement by default (--no-refine), maps and blobs, and that the model changes no processing
decision except the indexing choice on serial stills with -C/-S. It says plainly that the defaults
are meant to be the answer, and lists the output files with and without a model. The tutorial's
stills section drops -X ffbidx, -z and the resolution limit from its first example and shows the
same three stills commands.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit bfca846332037688364b9d2d1c4250315f09410d)

2026-10-26 15:23:07 +01:00

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Documentation

The manuals and reference of Jungfraujoch and Rugnux, open-source software from the Paul Scherrer Institute for X-ray diffraction data. The front page has the overview and the downloads; this page is the map of the documentation.

Data processing

Rugnux

Processes a stored macromolecular diffraction dataset, a rotation sweep or serial stills, from the images to merged data: spot finding, indexing, integration, scaling and merging, with the space group, cell and resolution decided from the data and a report that says on what evidence. Given an atomic model it goes on to a refined structure and maps: the model is placed (rigid body or molecular replacement) and refined against the merge. One command, no parameters.

rugnux <diffraction image file>
rugnux <diffraction image file> <CIF/PDB model file>

Linux · macOS · Windows · fast on an NVIDIA GPU, works without one

Get started Download What it does Manual

Desktop application

Jungfraujoch Viewer

Shows what is in a diffraction dataset: every image with its spots, predictions and resolution rings, per-image statistics over the sweep, grid-scan maps, and the same processing pipeline as Rugnux, run from a settings panel on the open file. Follows a live collection from a running Jungfraujoch broker.

Linux · macOS · Windows · Qt 6

Get started Download Guided tour

Data acquisition

Jungfraujoch

The data-acquisition and real-time analysis system for the PSI JUNGFRAU and EIGER detectors, and for DECTRIS detectors through their control unit: an FPGA and GPU pipeline that takes the detector's frames at full rate, analyses them on the fly, streams them to the NXmx HDF5 writer and serves a web interface and REST API to the beamline.

Linux servers · AMD Alveo U55C FPGA · NVIDIA GPUs

Get started Install Broker Writer

Licence. Rugnux, the viewer and the Jungfraujoch services are free software under the GNU General Public License v3 <LICENSE>; the FPGA design is released under the CERN Open Hardware Licence v2, strongly reciprocal <FPGA_LICENSE>. Both let anyone, in academia or industry, use, study and modify the software and the hardware design at no charge, commercial use included; what they ask is that a modified version which is passed on is shared under the same terms. The released binaries bundle third-party components under GPL-compatible licences, and the CUDA builds the NVIDIA CUDA runtime under NVIDIA's own EULA: see the third-party notices <THIRD_PARTY_NOTICES>.

All pages

Everything a user of Rugnux or the viewer needs comes first; the technical reference <TECHNICAL> holds the algorithms, the file formats and streams, the interfaces and the FPGA design. The names are explained in Naming <NAMING>, the releases in the changelog <CHANGELOG>.

Getting started <RUGNUX> Download <RUGNUX_DOWNLOAD> RUGNUX_OVERVIEW RUGNUX_INSTALL RUGNUX_FORMATS RUGNUX_TUTORIAL RUGNUX_REPORT RUGNUX_INTEGRATION RUGNUX_ADVANCED RUGNUX_MODEL_AND_REFERENCE Detector calibration <RUGNUX_CALIBRATION>

Using the viewer <JFJOCH_VIEWER> Download <VIEWER_DOWNLOAD>

Overview <JUNGFRAUJOCH> DEPLOYMENT REPOSITORIES RELEASE_CONTENTS JFJOCH_BROKER JFJOCH_WRITER WEB_FRONTEND MX software integration <SOFTWARE_INTEGRATION> TOOLS Python client <PYTHON_CLIENT>

TECHNICAL

ACKNOWLEDGEMENT LICENSE THIRD_PARTY_NOTICES NAMING CHANGELOG

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