<?xml version="1.0" encoding="UTF-8"?>
<!-- Copyright 2014-2024 Paul Emsley <pemsley@mrc-lmb.cam.ac.uk> -->
<component type="desktop">
  <id>io.github.pemsley.coot</id>
  <launchable type="desktop-id">io.github.pemsley.coot.desktop</launchable>
  <metadata_license>GFDL-1.3</metadata_license>
  <project_license>GPL-2.0+ and GPL-3.0+ and LGPL-3.0+</project_license>
  <name>Coot</name>
  <summary>Macromolecular model builder</summary>
  <description>
    <p>
      Coot is a powerful macromolecular model-building tool for
      analysing X-ray data and models (i.e. proteins, ligands, RNA and
      DNA). There are many tools for model manipulation and building,
      such as minimization, molecular superposition, fragment
      rotation/translations, rotamer-fitting, de novo building and
      refinement.
    </p>
    <p>
      Coot is used by scientists using X-ray crystallography or cryo-EM for
      analysis of proteins, electron density maps, protein interactions
      and drug design.
    </p>
  </description>
  <screenshots>
    <screenshot type="default">
      <image type="source">
        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/other/coot-viagra-1.png</image>
      <caption>Coot is typically used to view protein models and electron density</caption>
    </screenshot>
    <screenshot>
      <image type="source">
        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/other/coot-ligand-builder.png</image>
      <caption>Coot can be used to convert from 2D ligands to 3D and from 3D to 2D</caption>
    </screenshot>
    <screenshot>
      <image type="source">
        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/apoferritin/sapphires-and-emeralds.png</image>
    </screenshot>
  </screenshots>
  <branding>
    <color type="primary" scheme_preference="light">#dcc9c7</color>
    <color type="primary" scheme_preference="dark">#79170a</color>
  </branding>
  <url type="homepage">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/</url>
  <url type="faq">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/coot-faq.html</url>
  <url type="help">https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs</url>
  <url type="vcs-browser">https://github.com/pemsley/coot</url>
  <url type="bugtracker">https://github.com/pemsley/coot/issues</url>
  <developer id="io.github.pemsley">
    <name>Paul Emsley</name>
  </developer>
  <update_contact>pemsley_AT_mrc-lmb.cam.ac.uk</update_contact>
  <content_rating type="oars-1.1" />
  <releases>
    <release version="1.1.10" date="2024-07-21">
      <description>
        <ul>
          <li>FEATURE: Noughties-physics - add a refinement/atom manipulation mode so that Coot behaves like it used to up to (and including) version 0.8.x: `coot.set_refine_use_noughties_physics()`.</li>
          <li>FEATURE: Layla now displays QED Scores for molecules.</li>
          <li>FEATURE: `read_coordinates()` added to the Coot.</li>
          <li>FEATURE: Cryo-EM servalcat use added to the Coot API.</li>
          <li>CHANGE: Network download files now follow the XDG Base Directory Protocol.</li>
          <li>CHANGE: HUD Ramachandran Plot is now pickable.</li>
          <li>CHANGE: Ligands with no dictionary are drawn with bonds in "Colour by Chain" mode.</li>
          <li>CHANGE: Python requests is no longer a dependency.</li>
          <li>BUG-FIX: Scroll wheel indicator in the Display Manager now correctly updates on use of a key-binding to change the scrollable map.</li>
          <li>BUG-FIX: Ugly least-squares fit dialog has been modernized.</li>
          <li>BUG-FIX: Fix the callback actions for the "Display Hydrogen Atoms" in the Bonds control dialog.</li>
          <li>BUG-FIX: Rework the calculation of `pkg_data_dir()` - particularly in the case of relocatable binaries.</li>
        </ul>
      </description>
    </release>
  </releases>
</component>
