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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)
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Documentation
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=============
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.. raw:: html
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<p class="jfj-lead">The manuals and reference of Jungfraujoch and Rugnux, open-source software
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from the <a href="https://www.psi.ch">Paul Scherrer Institute</a> for X-ray diffraction data.
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The <a href="index.html">front page</a> has the overview and the downloads; this page is the
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map of the documentation.</p>
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<div class="jfj-cards">
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<div class="jfj-card">
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<p class="jfj-card__kicker">Data processing</p>
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<h2 class="jfj-card__title">Rugnux</h2>
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<p class="jfj-card__text">Processes a stored macromolecular diffraction dataset, a rotation
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sweep or serial stills, from the images to merged data: spot finding, indexing, integration,
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scaling and merging, with the space group, cell and resolution decided from the data and a
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report that says on what evidence. Given an atomic model it goes on to a refined structure and
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maps: the model is placed (rigid body or molecular replacement) and refined against the merge.
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One command, no parameters.</p>
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<pre class="jfj-card__run"><code>rugnux <diffraction image file>
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rugnux <diffraction image file> <CIF/PDB model file></code></pre>
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<p class="jfj-platforms">Linux · macOS · Windows · fast on an NVIDIA GPU,
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works without one</p>
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<p class="jfj-card__links"><a href="RUGNUX.html">Get started</a>
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<a href="RUGNUX_DOWNLOAD.html">Download</a>
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<a href="RUGNUX_OVERVIEW.html">What it does</a>
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<a href="RUGNUX_TUTORIAL.html">Manual</a></p>
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</div>
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<div class="jfj-card">
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<p class="jfj-card__kicker">Desktop application</p>
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<h2 class="jfj-card__title">Jungfraujoch Viewer</h2>
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<p class="jfj-card__text">Shows what is in a diffraction dataset: every image with its spots,
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predictions and resolution rings, per-image statistics over the sweep, grid-scan maps, and
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the same processing pipeline as Rugnux, run from a settings panel on the open file. Follows a
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live collection from a running Jungfraujoch broker.</p>
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<p class="jfj-platforms">Linux · macOS · Windows · Qt 6</p>
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<p class="jfj-card__links"><a href="JFJOCH_VIEWER.html">Get started</a>
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<a href="VIEWER_DOWNLOAD.html">Download</a>
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<a href="JFJOCH_VIEWER.html#a-guided-tour">Guided tour</a></p>
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</div>
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<div class="jfj-card">
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<p class="jfj-card__kicker">Data acquisition</p>
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<h2 class="jfj-card__title">Jungfraujoch</h2>
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<p class="jfj-card__text">The data-acquisition and real-time analysis system for the PSI
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JUNGFRAU and EIGER detectors, and for DECTRIS detectors through their control unit: an FPGA
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and GPU pipeline that takes the detector's frames at full rate, analyses them on the fly,
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streams them to the NXmx HDF5 writer and serves a web interface and REST API to the
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beamline.</p>
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<p class="jfj-platforms">Linux servers · AMD Alveo U55C FPGA · NVIDIA GPUs</p>
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<p class="jfj-card__links"><a href="JUNGFRAUJOCH.html">Get started</a>
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<a href="DEPLOYMENT.html">Install</a>
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<a href="JFJOCH_BROKER.html">Broker</a>
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<a href="JFJOCH_WRITER.html">Writer</a></p>
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</div>
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</div>
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**Licence.** Rugnux, the viewer and the Jungfraujoch services are free software under the
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:doc:`GNU General Public License v3 <LICENSE>`; the FPGA design is released under the
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:doc:`CERN Open Hardware Licence v2, strongly reciprocal <FPGA_LICENSE>`. Both let anyone, in
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academia or industry, use, study and modify the software and the hardware design at no charge,
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commercial use included; what they ask is that a modified version which is passed on is shared
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under the same terms. The released binaries bundle third-party components under GPL-compatible
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licences, and the CUDA builds the NVIDIA CUDA runtime under NVIDIA's own EULA: see the
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:doc:`third-party notices <THIRD_PARTY_NOTICES>`.
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All pages
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---------
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Everything a user of Rugnux or the viewer needs comes first; the :doc:`technical reference <TECHNICAL>`
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holds the algorithms, the file formats and streams, the interfaces and the FPGA design. The names
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are explained in :doc:`Naming <NAMING>`, the releases in the :doc:`changelog <CHANGELOG>`.
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.. raw:: html
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<div class="jfj-sitemap">
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.. toctree::
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:maxdepth: 1
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:caption: Rugnux
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Getting started <RUGNUX>
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Download <RUGNUX_DOWNLOAD>
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RUGNUX_OVERVIEW
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RUGNUX_INSTALL
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RUGNUX_FORMATS
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RUGNUX_TUTORIAL
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RUGNUX_REPORT
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RUGNUX_INTEGRATION
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RUGNUX_ADVANCED
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RUGNUX_MODEL_AND_REFERENCE
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Detector calibration <RUGNUX_CALIBRATION>
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.. toctree::
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:maxdepth: 1
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:caption: Jungfraujoch Viewer
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Using the viewer <JFJOCH_VIEWER>
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Download <VIEWER_DOWNLOAD>
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.. toctree::
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:maxdepth: 1
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:caption: Jungfraujoch
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Overview <JUNGFRAUJOCH>
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DEPLOYMENT
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REPOSITORIES
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RELEASE_CONTENTS
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JFJOCH_BROKER
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JFJOCH_WRITER
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WEB_FRONTEND
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MX software integration <SOFTWARE_INTEGRATION>
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TOOLS
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Python client <PYTHON_CLIENT>
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.. toctree::
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:maxdepth: 1
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:caption: Reference
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TECHNICAL
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.. toctree::
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:maxdepth: 1
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:caption: Project
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ACKNOWLEDGEMENT
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LICENSE
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THIRD_PARTY_NOTICES
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NAMING
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CHANGELOG
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.. raw:: html
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</div>
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