leonarski_fandClaude Opus 5.5
f81c0c7f0f
- docs/PUBLICATIONS.md: how to cite (Rugnux: bioRxiv 2026 preprint; Jungfraujoch: J. Synchrotron
Rad. 2023 stays primary, J. Appl. Cryst. 2026 for real-time serial / live indexing) and the
paper list (IUCrJ 2023 MAX IV, Struct. Dyn. 2020, TORO J. Appl. Cryst. 2024); linked from the
toctree, ACKNOWLEDGEMENT, README, RUGNUX and JUNGFRAUJOCH pages. All DOIs checked on Crossref.
- Landing page: a Publications band with two typeset title-page cards (Rugnux preprint and the
J. Appl. Cryst. paper, with the 2023 primary reference), nav and footer links; HTML/CSS only, no
logos or images.
- rugnux prints a one-line citation in its startup banner (fits the 78-column console) and the
full reference ("If you find rugnux useful, please cite ...") at the head of _report.txt.
- Files jfjoch_writer writes from Rugnux live mode name both programs: the MTZ files get a
"From Jungfraujoch <version>, data collection" HISTORY record after Rugnux's (and a Rugnux
record where the map tables carry none), the placed/refined model mmCIF get Rugnux
(phasing/refinement) and Jungfraujoch (data collection) in _software. The round-trip tests
expect those additions.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQqrMy3Kh9NQw823gEb
5.1 KiB
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
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
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
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>,
and how to cite the software in Publications <PUBLICATIONS>.
Getting started <RUGNUX> Download <RUGNUX_DOWNLOAD> RUGNUX_OVERVIEW RUGNUX_INSTALL RUGNUX_FORMATS RUGNUX_TUTORIAL RUGNUX_CLI 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
PUBLICATIONS ACKNOWLEDGEMENT LICENSE THIRD_PARTY_NOTICES NAMING CHANGELOG