coot.appdata.xml

<?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="1.1.20" date="2025-11-29">
      <description>
        <ul>

          <li> o FEATURE: "New Residue Type" now available in Add Other
                           Solvents dialog</li>

          <li> o FEATURE: key-binding for Triple-Refine AA (H)</li>

          <li> o FEATURE: key-binding for Undo Symmetry View (Shift V)</li>

          <li> o FEATURE: key-binding for Keyboard Mutate (Shift-M)</li>

          <li> o FEATURE: now Open Dialogs track the latest used directory</li>

          <li> o FEATURE: "Unhappy Atom" markup added</li>

          <li> o FEATURE: Add keyboard mutate</li>

          <li> o FEATURE: Add user-defined type to "Add Other Solvent Molecule"
                          dialog</li>

          <li> o FEATURE: on initial startup, Coot will ask if left-mouse
          should be used for view rotation</li>

          <li> o FEATURE: (Multi) Pick Delete Atom added</li>

          <li> o FEATURE: Bad Non-bonded contact markers now have dashed lines
                          between the atoms</li>

          <li> o FEATURE: The space group info is now displayed in log on reading
                          a coordinates file</li>

          <li> o FEATURE: Now configuration with --sound works</li>

          <li> o FEATURE: Other types of Carbohydrate added (back)</li>

          <li> o FEATURE: server mode turned into JSON RPC server</li>

          <li> o CHANGE:  XDG is used for the download of COD entries</li>

          <li> o CHANGE:  Update the "No Unmodelled Blobs" dialog</li>

          <li> o CHANGE:  Update the url for AlphaFold models to v6</li>

          <li> o CHANGE:  User-feedback when trying to rotate unselected chi angle
                          improved</li>

          <li> o CHANGE:  Cross-hairs have fixed size, not relative size - the
                          size is configurable in Preferences</li>

          <li> o CHANGE:  "Environment Distances" is now a transient [Oliver Clarke]</li>

          <li> o CHANGE:  CA Label now follow the residue on "Space" repositioning</li>

          <li> o CHANGE:  Recentre on new fragment on "Copy Fragment"</li>

          <li> o CHANGE:  Overlay notification on B-factor and Occupancy updated</li>

          <li> o CHANGE:  B-factor and Occupancy modification now has an overlay
                          notifier</li>

          <li> o BUG-FIX: "Undo molecule" dialog operation fixed</li>

          <li> o BUG-FIX: Display Control dialog is only displayed on restart
                          if it was displayed on session save</li>

          <li> o BUG-FIX: fix control of display control dialog in the
                          state script</li>

          <li> o BUG-FIX: fix missing protein-ligand interactions for FLEV
                          [thanks Lan Guan]</li>

          <li> o BUG-FIX: set_molecule_name() function for models fixed</li>

          <li> o BUG-FIX: one can now no longer pick/drag undisplayed intermediate
                          hydrogen atoms [thanks Oliver Clarke]</li>

          <li> o BUG-FIX: the "No Unmodelled blobs" dialog tided up</li>

          <li> o BUG-FIX: get-monomer dialog activate now closes the drop-down.</li>

          <li> o BUG-FIX: undisplay "Get monomer" frame on entry activate</li>

          <li> o NEW FUNCTION: get_mmrrcc()</li>

          <li> o NEW FUNCTION: get_residue_pucker_info() function added</li>

        </ul>
      </description>
    </release>

    <release version="1.1.19" date="2025-10-07">
      <description>
        <ul>
           <li> o FEATURE: Double-click to label symmetry atoms</li>
           <li> o FEATURE: drag-and-drop import for local-file-system files</li>
           <li> o CHANGE:  user-defined-clicks added back</li>
           <li> o CHANGE:  Assign and Associate Sequence menu items functions now added back</li>
           <li> o CHANGE:  Improve the scrolling of the map contour level when the
                  nominated map is not displayed</li>
           <li> o BUG-FIX: Menu items with targets don't work on macOS (I don't know why).
            The targets have been removed, so these menu items should now
            work again (e.g. Fetch and Mutate menu items)</li>
        </ul>
      </description>
    </release>
    <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>