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<title>Jungfraujoch and Rugnux: X-ray diffraction data, from the detector to merged data and refined structures</title>
<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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  <a class="brand" href="index.html"><img src="_static/jfjoch.png" alt="" width="36" height="33"><span>Jungfraujoch</span></a>
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    <a href="#programs">Programs</a>
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<section class="hero">
  <figure class="hero__art">
    <img class="hero__art-light" src="hero_live_light.webp" width="1120" height="848"
         alt="A diffraction image beside the placed model in its electron density, over the timeline of the live analysis: the detector lane of an 18 s collection and the Rugnux lane ending 4.9 s after the last image">
    <img class="hero__art-dark" src="hero_live_dark.webp" width="1120" height="848" alt="">
    <figcaption>Cytochrome C at SLS X10SA: 1800 images at 100&nbsp;Hz, merged and the AlphaFold model placed 4.9&nbsp;s after the last image</figcaption>
  </figure>
  <div class="hero__text">
    <p class="eyebrow">Paul Scherrer Institute &middot; open source</p>
    <h1>From the detector to merged data and refined structures.</h1>
    <p class="lede">Software for X-ray diffraction data: <strong>Rugnux</strong> takes a stored
    dataset from the images to merged data with one command, and with a model on to a refined
    structure and maps; the <strong>Viewer</strong> shows what is in it, and
    <strong>Jungfraujoch</strong> acquires it from the detector at full speed.</p>
    <div class="hero__actions">
      <a class="btn btn--primary" href="#download">Download</a>
      <a class="btn btn--ghost" href="documentation.html">Read the documentation</a>
    </div>
    <p class="hero__run"><code>rugnux &lt;diffraction image file&gt;</code><code>rugnux &lt;diffraction image file&gt; &lt;CIF/PDB model file&gt;</code></p>
  </div>
</section>

<section class="programs" id="programs">
  <div class="programs__grid">

    <article class="program">
      <p class="program__kicker">Data processing</p>
      <h2>Rugnux</h2>
      <p>Takes a macromolecular diffraction dataset, a synchrotron rotation sweep or XFEL 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. Writes <code>.mtz</code>, <code>.cif</code> and <code>.hkl</code> for the programs
      that come next. Given an atomic model it goes on to a refined structure: the model is placed
      (as a rigid body or by molecular replacement) and refined, and the maps and the unexplained
      difference-density blobs are written beside it. Validated on public data:
      <a href="EXTERNAL_TEST_DATA.html">over 200 rotation datasets</a> and
      <a href="EXTERNAL_TEST_DATA_STILLS.html">eleven XFEL serial datasets</a>.</p>
      <p class="program__meta">Linux &middot; macOS &middot; Windows &middot; command line &middot; fast on an NVIDIA GPU, works without one</p>
      <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>
    </article>

    <article class="program">
      <p class="program__kicker">Desktop application</p>
      <h2>Jungfraujoch Viewer</h2>
      <p>Shows what is in a 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.</p>
      <p class="program__meta">Linux &middot; macOS &middot; Windows &middot; Qt 6</p>
      <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>
    </article>

    <article class="program">
      <p class="program__kicker">Data acquisition</p>
      <h2>Jungfraujoch</h2>
      <p>The 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.</p>
      <p class="program__meta">Linux servers &middot; AMD Alveo U55C FPGA &middot; NVIDIA GPUs</p>
      <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>
    </article>

  </div>
</section>

<section class="download" id="download">
  <div class="download__head">
    <h2>Download</h2>
    <p>Pre-built, signed where the platform asks for it, nothing to install beside them.
    <span data-os-note></span></p>
  </div>

  <div class="download__program" id="dl-rugnux">
    <h3>Rugnux</h3>
    <p>One self-contained executable. Unpack the archive into a directory of its own and run
    <code>bin/rugnux</code>; no CUDA toolkit, no Qt, no service. On a machine with an NVIDIA GPU
    take the GPU build, which also runs without one. <a href="RUGNUX_DOWNLOAD.html">Details, packages and building from source</a>.</p>
    {{downloads:rugnux}}
  </div>

  <div class="download__program" id="dl-viewer">
    <h3>Jungfraujoch Viewer</h3>
    <p>A desktop application with the Qt runtime included: a portable archive on Linux, a
    notarized disk image on macOS, an installer on Windows. <a href="VIEWER_DOWNLOAD.html">Details and building from source</a>.</p>
    {{downloads:viewer}}
  </div>

  <div class="download__program download__program--text">
    <h3>Jungfraujoch, the acquisition system</h3>
    <p>Installed on the beamline's Linux servers from the <a href="REPOSITORIES.html">RPM and APT
    repositories</a> (<code>jfjoch</code>, <code>jfjoch-writer</code>, <code>jfjoch-driver-dkms</code>,
    <code>jfjoch-viewer</code>, <code>rugnux</code>), with the FPGA firmware and the writer's
    packages attached to every <a href="https://gitea.psi.ch/mx/jungfraujoch/releases">release</a>.
    <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>
  </div>
</section>

<section class="licence">
  <h2>Free to use, in academia and industry</h2>
  <p>Rugnux, the viewer and the Jungfraujoch services are free software under the
  <a href="LICENSE.html">GNU General Public License v3</a>; the FPGA design is released under the
  <a href="FPGA_LICENSE.html">CERN Open Hardware Licence v2, strongly reciprocal</a>. Both let
  anyone 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 EULA: see the
  <a href="THIRD_PARTY_NOTICES.html">third-party notices</a>.</p>
</section>

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  <a href="ACKNOWLEDGEMENT.html">acknowledgements</a> &middot; <a href="https://gitea.psi.ch/mx/jungfraujoch">source</a></p>
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