leonarski_f
a9d5367013
* Rugnux: Several rotation sweeps of one crystal are merged as one dataset (`rugnux a_master.h5 b_master.h5`), on a common indexing and cell, with a non-isomorphous sweep left out and reported; `--sweeps separate` processes each sweep on its own. Bruker `.sfrm` frames and imgCIF files with a full goniometer axis chain are read. * Rugnux: More robust rotation processing - a retry with a more sensitive spot finder when no lattice is found, a self-consistent detector distance, long axes and doubled cells tested as hypotheses, a `-C` supercell multiple stepped down, and each ice ring merged, down-weighted or rejected on its own. * Rugnux: Serial stills are merged with a partiality-aware error model, reported as `ERROR_MODEL_A/B/C` with no ISa or R_merge/R_meas/R_pim; runs without `-S` have an overall intensity scale about 0.86-0.88 times that of earlier versions, with unchanged statistics. A second crystal form is left out of the merge and reported, the indexing ambiguity is resolved more reliably, and `--model` no longer influences processing. * Rugnux: The reported CC1/2 is the standard unweighted one, which can be lower than before on sweeps with weak frames; ISa comes with a 95% interval (`ISA_LOW`/`ISA_HIGH`). * Rugnux: Model refinement adds anisotropic/TLS, local NCS and twin refinement where R-free supports them; building waters and relabelling ions is now off by default (`--refine-solvent` turns it on). * NXmx: A detector of several modules is written as `module_0` ... `module_N` only, so DIALS reads each module as its own panel. * Other: JPEG previews use a bundled encoder (libjpeg-turbo no longer needed), Rugnux prints how to cite it, and the release archives contain the HTML documentation. Reviewed-on: #92 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
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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
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