<?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/coot1/coot1_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/coot1/coot1_2.png</image>
    </screenshot>
    <screenshot>
      <image type="source">
        https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/screenshots/coot1/coot1_12.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="1.1.18" date="2025-08-01">
      <description>
        <ul>
           <li> o FEATURE: Ctrl-F keybinding added to smooth the bonds </li>
           <li> o FEATURE: Multi-select for opening maps </li>
           <li> o FEATURE: "Side-chain 180°" button now does syn/anti flip for nucleotides </li>
           <li> o FEATURE: "Split Water" added to Modelling menu </li>
           <li> o CHANGE:  "Copy Fragment" has become an overlay </li>
           <li> o CHANGE:  "Move Molecule Here" has become an overlay </li>
           <li> o CHANGE:  Generic Display Objects can now have translation gizmos </li>
           <li> o CHANGE:  layla now has relocatable directory support </li>
           <li> o CHANGE:  Monomer-library look-up reworked</li>
           <li> o BUG-FIX: Removed bug in parsing external torsion restraints </li>
           <li> o BUG-FIX: Curlew has moved to use XDG Base Directory specs </li>
        </ul>
      </description>
    </release>
    <release version="1.1.17" date="2025-06-14">
      <description>
        <ul>
          <li> o BUG-FIX: Save symmetry coordinates is fixed </li>
          <li> o BUG-FIX: Colour-by-B-factor colours are fixed </li>
          <li> o BUG-FIX: Place atom at pointer fixed </li>
          <li> o BUG-FIX: Optional Gemmi usage restored </li>
        </ul>
      </description>
    </release>
    <release version="1.1.16" date="2025-06-04">
      <description>
        <ul>
          <li> o FEATURE: Local B-factor display </li>
          <li> o FEATURE: Built-in logging (started) - view it by clicking the "Log" button</li>
          <li> o FEATURE: Full doxygen documentation transfered to chapi nanobind functions</li>
          <li> o FEATURE: Anisotropic probability radius scaling (thank ClAuS Flensburg)</li>
          <li> o CHANGE: For packagers: Now a commonly-used fragment of the monomer library
            is bundled with Coot. Unknown monomers are now downloaded from GitHub
            and cached using XDG Base Directory Specification</li>
          <li> o CHANGE:  For packagers: Now the reference structures are bundled
            with the source code (and installed) - no longer do they need
            to be a separate dependency</li>
          <li> o CHANGE:  If a map has a PANDDA:: or APPLY-SYMMETRY:: label then Coot now
            properly handles that (turns off "is-EM-map" status)</li>
          <li> o CHANGE:  Atoms with Zero Occupancy results now moved into the
            main window</li>
          <li> o CHANGE:  Boron atoms are now pinky-beige - like Jmol</li>
          <li> o BUG-FIX: Fix crash on adding an atom [Clément Bousquet]</li>
          <li> o BUG-FIX: Symmetry atoms are now clickable for distances and labels</li>
          <li> o BUG-FIX: Fix the non-drawn clashes post model update</li>
          <li> o BUG-FIX: "Add Other Solvent Molecules" dialog has been depythonized
            and now will work on macOS</li>
          <li> o BUG-FIX: "Copy Molecule" dialog has been depythonized and is now an
            overlay and now will work on macOS</li>
          <li> o BUG-FIX: Fix the problem of focus-grab when using Tutorial Model &amp; Data</li>
          <li> o BUG-FIX: Fix the "Close" button in the Restraints Editor</li>
        </ul>
      </description>
    </release>
    <release version="1.1.15" date="2025-06-04">
      <description>
        <ul>
          <li> o FEATURE: Drag and drop (partial - it works from the file browser,</li>
            but not from CCP4i2)
          <li> o FEATURE: set_use_vertex_gradients_for_map_normals() added to the Coot API</li>
          <li> o CHANGE:  Fixed atoms are now draggable</li>
          <li> o CHANGE:  max-closeness is no longer used to filter peaks in map_peaks_py()</li>
          <li> o CHANGE:  Backtick for selection now also shows the residue range
            (if set)</li>
          <li> o BUG-FIX: Track-pad zooming fixed</li>
          <li> o BUG-FIX: Residue Info dialog buttons now on the right hand side</li>
          <li> o BUG-FIX: Fix and Unfix atom now work as expected</li>
          <li> o BUG-FIX: Remove erroneous "No ligands Found" dialog when ligand fitting</li>
          <li> o BUG-FIX: Select Map for Fitting dialog now behaves has expected
            on reopen</li>
          <li> o BUG-FIX: Merge Molecules dialog now behaves has expected on reopen</li>
          <li> o BUG-FIX: Choose a better contour level for masked maps</li>
        </ul>
      </description>
    </release>
    <release version="1.1.14" date="2025-03-16">
      <description>
        <ul>
          <li>FEATURE: Clark and Labute-like 2D-ligand environment view in Coot,
             Moorhen and chapi.</li>
          <li>FEATURE: Symmetry represented as solid model (no longer just lines)</li>
          <li>FEATURE: new chapi functions: `is_nucleic_acid()` and `delete_all_carbohydrate()`</li>
          <li>FEATURE: PAE Plots on downloading Alphafold models.</li>
          <li>FEATURE: 3D symmetry.</li>
          <li>CHANGE: Setting the primary mouse button for view rotation enables
             secondary mouse button for zoom (like Old Coot).</li>
          <li>CHANGE: chapi modules name now changed to coot_headless_api
          so that the molecules_container object can be called
          chapi.</li>
          <li>CHANGE: Alphafold downloads are now XDG Base Directory compliant.</li>
          <li>BUG-FIX: NCS Jumping has been fixed -  Bernhard Lohkamp.</li>
          <li>BUG-FIX: unwritable XDG cache dir now longer causes a crash
             [Jordan Dialpuri].</li>
          <li>BUG-FIX: Shader for drawing ribbons.</li>
          <li>BUG-FIX: About and Preferences dialogs can now be properly closed.</li>
          <li>BUG-FIX: Texture handling for bad NBC markers updated [Fixes crash].</li>
        </ul>
      </description>
    </release>
    <release version="1.1.13" date="2025-02-24">
      <description>
        <ul>
          <li>FEATURE: New chapi functions added: `get_svg_for_2d_ligand_environment_view()`, `get_HOLE()`, and `scale_map()`. Additionally, nucleic acids now work with `add_terminal_residue()` and sticks and dishy bases are not drawn for atoms not in selection.</li>
          <li>FEATURE: Non-drawn maps are not recontoured on view translation; they now wait until the map is displayed. [Elegant-Land-8008]</li>
          <li>FUNCTION-RESTORED: When "Spacing" along a chain, the CA label follows.</li>
          <li>FUNCTION-RESTORED: SSM dialog now works.</li>
          <li>FUNCTION-RESTORED: NCS Ghosts dialog now works.</li>
          <li>BUG-FIX: Missing shader for instanced geometry for SSAO added back.</li>
          <li>COMPILATION: Issue for `graphics_info_t::scale_up_graphics` has been resolved.</li>
        </ul>
      </description>
    </release>
    <release version="1.1.12" date="2025-02-11">
      <description>
        <ul>
          <li>TERMINAL OUTPUT: Increased diagnostic output on startup to help troubleshoot graphics
            and Python issues across diverse operating systems, drivers, and Python versions.</li>
          <li>FEATURE: New chapi functions added: `add_terminal_residue_directly()`,
            `copy_molecule()`, `flood()`, `get_validation_vs_dictionary_for_selection()`,
            `servalcat_refine_xray()`, `get_torsion()`, `change_alt_locs()`,
            `split_residue_using_map()`, `get_missing_residue_ranges()`, `get_mutation_info()`, and
            `set_temperature_factor_using_cid()` (see Pythonic and C++ API documentation).</li>
          <li>FEATURE: New Coot API functions added: `set_new_non_drawn_bonds()` and
            `add_new_non_draw_bonds()`.</li>
          <li>FEATURE: Graphics viewport scaling added.</li>
          <li>FEATURE: Acedrg link interface added.</li>
          <li>FEATURE: HOLE interface restored.</li>
          <li>FEATURE: Transform map by LSQ model fit restored.</li>
          <li>BUG-FIX: '--code &lt;accession-code&gt;' now functions correctly following the XDG
            Directory Protocol update.</li>
          <li>BUG-FIX: Resolved the no-recentre-view issue in the coordinate file open dialog.</li>
          <li>BUG-FIX: Contact dots for ligands now correctly display ligand donor to water hydrogen
            bonds.</li>
          <li>BUG-FIX: Disabled refinement using a CCD dictionary (thanks to Lorenzo Masso).</li>
          <li>BUG-FIX: Correct shader usage implemented for surfaces in "Plain" mode.</li>
          <li>BUG-FIX: LSQ Fit dialog functionality restored.</li>
          <li>BUG-FIX: Prevented CYS with hydrogen atoms from forming spurious disulfide bonds
            (thanks to Jordan Dialpuri).</li>
          <li>BUG-FIX: End-of-chain TER atom removal on adding a new terminal residue fixed.</li>
          <li>BUG-FIX: Dark mode icons now display correctly in Layla.</li>
          <li>BUG-FIX: Startup window width increased on macOS for better usability.</li>
          <li>BUG-FIX: Global Phasing column labels (F_early-late) now auto-read.</li>
          <li>BUG-FIX: Hydrogen atom deletion in Layla now works properly.</li>
          <li>CHANGE: Framebuffer usage reduced/removed in --opengl-es mode.</li>
          <li>CHANGE: Module menus now depthonized.</li>
          <li>CHANGE: Overlay added for the Cryo-EM "Flip Hand" tool.</li>
          <li>CHANGE: Pythonic startup process updated for improved performance.</li>
          <li>KNOWN BUG: Ramachandran Plot display issues persist on some macOS systems.</li>
        </ul>
      </description>
    </release>
    <release version="1.1.11" date="2024-12-12">
      <description>
        <ul>
          <li>FEATURE: One can now dynamically edit SMILES in layla.</li>
          <li>FEATURE: Anisotropic atom representation [thanks to Global Phasing].</li>
          <li>FEATURE: Better linking across sequence gaps in RNA and DNA.</li>
          <li>FEATURE: Electrostatic representation [Stuart McNicholas].</li>
          <li>FEATURE: Acedrg atom types are now parsed from dictionaries.</li>
          <li>FEATURE: Function `partition_map_by_chain()` added.</li>
          <li>OTHER: Various non-user-visible changes for Flatpak compatibility.</li>
        </ul>
      </description>
    </release>
    <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>
