leonarski_f
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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)
157 lines
9.4 KiB
HTML
157 lines
9.4 KiB
HTML
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<title>Jungfraujoch and Rugnux: X-ray diffraction data, from the detector to merged data and refined structures</title>
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<meta name="description" content="Open-source software from the Paul Scherrer Institute: Rugnux processes macromolecular diffraction data with one command, to merged data and, with a model, a refined structure, the Jungfraujoch Viewer shows it, and Jungfraujoch acquires it from JUNGFRAU and EIGER detectors at full speed.">
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<body>
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<header class="top">
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<a class="brand" href="index.html"><img src="_static/jfjoch.png" alt="" width="36" height="33"><span>Jungfraujoch</span></a>
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<nav class="top__nav" aria-label="Sections">
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<a href="#programs">Programs</a>
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<a href="#download">Download</a>
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<a href="documentation.html">Documentation</a>
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<a href="https://gitea.psi.ch/mx/jungfraujoch">Source</a>
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<button class="theme-toggle" type="button" aria-label="Switch between light and dark theme" title="Light / dark">
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<svg class="theme-toggle__sun" viewBox="0 0 24 24" width="20" height="20" aria-hidden="true"><circle cx="12" cy="12" r="4.5" fill="none" stroke="currentColor" stroke-width="2"/><path d="M12 2v3M12 19v3M2 12h3M19 12h3M4.9 4.9l2.1 2.1M17 17l2.1 2.1M4.9 19.1 7 17M17 7l2.1-2.1" stroke="currentColor" stroke-width="2" stroke-linecap="round"/></svg>
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</header>
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<main>
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<section class="hero">
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<figure class="hero__art">
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<img src="hero_frame.webp" width="920" height="920" alt="A diffraction image: rows of Bragg spots, the beam stop's shadow and the gaps between detector modules"
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title="Lysozyme, one 0.2° rotation frame on an EIGER2 16M, SLS beamline X10SA, Paul Scherrer Institute">
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<figcaption>Lysozyme · one 0.2° frame · EIGER2 16M · SLS X10SA</figcaption>
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</figure>
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<div class="hero__text">
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<p class="eyebrow">Paul Scherrer Institute · open source</p>
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<h1>From the detector to merged data and refined structures.</h1>
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<p class="lede">Software for X-ray diffraction data: <strong>Rugnux</strong> takes a stored
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dataset from the images to merged data with one command, and with a model on to a refined
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structure and maps; the <strong>Viewer</strong> shows what is in it, and
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<strong>Jungfraujoch</strong> acquires it from the detector at full speed.</p>
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<div class="hero__actions">
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<a class="btn btn--primary" href="#download">Download</a>
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<a class="btn btn--ghost" href="documentation.html">Read the documentation</a>
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</div>
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<p class="hero__run"><code>rugnux <diffraction image file></code><code>rugnux <diffraction image file> <CIF/PDB model file></code></p>
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</div>
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</section>
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<section class="programs" id="programs">
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<div class="programs__grid">
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<article class="program">
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<p class="program__kicker">Data processing</p>
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<h2>Rugnux</h2>
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<p>Takes a macromolecular diffraction dataset, a rotation sweep or serial stills, from the
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images to merged data: spot finding, indexing, integration, scaling and merging, with the
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space group, cell and resolution decided from the data and a report that says on what
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evidence. Writes <code>.mtz</code>, <code>.cif</code> and <code>.hkl</code> for the programs
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that come next. Given an atomic model it goes on to a refined structure: the model is placed
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(as a rigid body or by molecular replacement) and refined, and the maps and the unexplained
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difference-density blobs are written beside it.</p>
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<p class="program__meta">Linux · macOS · Windows · command line · fast on an NVIDIA GPU, works without one</p>
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<p class="program__links"><a href="RUGNUX.html">Get started</a><a href="RUGNUX_OVERVIEW.html">What it does</a><a href="RUGNUX_TUTORIAL.html">Manual</a><a href="#dl-rugnux">Download</a></p>
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</article>
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<article class="program">
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<p class="program__kicker">Desktop application</p>
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<h2>Jungfraujoch Viewer</h2>
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<p>Shows what is in a dataset: every image with its spots, predictions and resolution rings,
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per-image statistics over the sweep, grid-scan maps, and the same processing pipeline as
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Rugnux, run from a settings panel on the open file. Follows a live collection from a running
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Jungfraujoch broker.</p>
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<p class="program__meta">Linux · macOS · Windows · Qt 6</p>
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<p class="program__links"><a href="JFJOCH_VIEWER.html">Get started</a><a href="JFJOCH_VIEWER.html#a-guided-tour">Guided tour</a><a href="#dl-viewer">Download</a></p>
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</article>
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<article class="program">
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<p class="program__kicker">Data acquisition</p>
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<h2>Jungfraujoch</h2>
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<p>The acquisition and real-time analysis system for the PSI JUNGFRAU and EIGER detectors,
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and for DECTRIS detectors through their control unit: an FPGA and GPU pipeline that takes
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the detector's frames at full rate, analyses them on the fly, streams them to the NXmx HDF5
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writer and serves a web interface and REST API to the beamline.</p>
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<p class="program__meta">Linux servers · AMD Alveo U55C FPGA · NVIDIA GPUs</p>
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<p class="program__links"><a href="JUNGFRAUJOCH.html">Get started</a><a href="DEPLOYMENT.html">Install</a><a href="JFJOCH_BROKER.html">Broker</a><a href="JFJOCH_WRITER.html">Writer</a></p>
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</article>
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</div>
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</section>
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<section class="download" id="download">
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<div class="download__head">
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<h2>Download</h2>
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<p>Pre-built, signed where the platform asks for it, nothing to install beside them.
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<span data-os-note></span></p>
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</div>
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<div class="download__program" id="dl-rugnux">
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<h3>Rugnux</h3>
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<p>One self-contained executable. Unpack the archive into a directory of its own and run
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<code>bin/rugnux</code>; no CUDA toolkit, no Qt, no service. On a machine with an NVIDIA GPU
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take the GPU build, which also runs without one. <a href="RUGNUX_DOWNLOAD.html">Details, packages and building from source</a>.</p>
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{{downloads:rugnux}}
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</div>
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<div class="download__program" id="dl-viewer">
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<h3>Jungfraujoch Viewer</h3>
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<p>A desktop application with the Qt runtime included: a portable archive on Linux, a
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notarized disk image on macOS, an installer on Windows. <a href="VIEWER_DOWNLOAD.html">Details and building from source</a>.</p>
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{{downloads:viewer}}
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</div>
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<div class="download__program download__program--text">
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<h3>Jungfraujoch, the acquisition system</h3>
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<p>Installed on the beamline's Linux servers from the <a href="REPOSITORIES.html">RPM and APT
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repositories</a> (<code>jfjoch</code>, <code>jfjoch-writer</code>, <code>jfjoch-driver-dkms</code>,
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<code>jfjoch-viewer</code>, <code>rugnux</code>), with the FPGA firmware and the writer's
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packages attached to every <a href="https://gitea.psi.ch/mx/jungfraujoch/releases">release</a>.
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<a href="DEPLOYMENT.html">Deployment</a> is the step-by-step guide; <a href="RELEASE_CONTENTS.html">Release contents</a> says what each package needs on the machine.</p>
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</div>
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</section>
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<section class="licence">
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<h2>Free to use, in academia and industry</h2>
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<p>Rugnux, the viewer and the Jungfraujoch services are free software under the
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<a href="LICENSE.html">GNU General Public License v3</a>; the FPGA design is released under the
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<a href="FPGA_LICENSE.html">CERN Open Hardware Licence v2, strongly reciprocal</a>. Both let
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anyone use, study and modify the software and the hardware design at no charge, commercial use
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included; what they ask is that a modified version which is passed on is shared under the same
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terms. The released binaries bundle third-party components under GPL-compatible licences, and the
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CUDA builds the NVIDIA CUDA runtime under NVIDIA's EULA: see the
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<a href="THIRD_PARTY_NOTICES.html">third-party notices</a>.</p>
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</section>
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</main>
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<footer class="foot">
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<p>Documentation for Jungfraujoch {{release}} · <a href="CHANGELOG.html">changelog</a> ·
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<a href="documentation.html">documentation</a> · <a href="NAMING.html">why the names</a> ·
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<a href="ACKNOWLEDGEMENT.html">acknowledgements</a> · <a href="https://gitea.psi.ch/mx/jungfraujoch">source</a></p>
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<p>© Paul Scherrer Institute. Jungfraujoch streams, Rugnux processes: two Swiss mountains, two railways, one idea of throughput.</p>
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