What’s New in Coot – October 2025 and Beyond

The Coot project has seen a steady stream of updates since October 2025, spanning new features, bug fixes, improvements to usability, and under-the-hood tweaks. Below we summarize the highlights and directions from more than 250 changes, as reflected in commit messages and RELEASE note updates. (Tip: browse all recent commits.)

🧪 Integration and Extensions

  • RDKit Experimentation: Several attempts were made to add new methods for generating or manipulating RDKit molecules directly within Coot, although challenges remain (details).
  • coot-headless-api: Now links with RDKit directly, improving computational ligand handling away from the GUI (details).

🧰 GUI, Usability, and Workflow

  • Improved Translation Gizmo: The translation gizmo’s visibility logic was overhauled—aimed at delivering a more robust and predictable user experience (details).
  • Rotamer Dialog: UI spacing for the close button was improved for more professional dialog layouts.
  • Contour Level Output: The contour_level_scroll_scrollable_map() method now prints additional information, making map interpretation easier (details).
  • Drag and Drop: “File” support was added for drag-and-drop operations in the UI (details).
  • Whitespace Clean-up: Multiple files received whitespace and style clean-up, reflecting a push for more readable code.

🧬 Ligand Validation and Chemistry

  • InChIKey Store: Added an internal store for InChIKeys and a key-binding for “go-to-ligand,” directly improving ligand navigation (details).
  • Ligand Validation Updates: Several internal updates made ligand validation and debugging more transparent for those developing or maintaining chemistry features (details).

📝 Documentation & Release Notes

  • Doxygen Integration: Added a warning for a missing Doxygen XML file—helpful for developers generating API docs (details).
  • RELEASE Notes: Trivial but frequent updates and typo fixes; the team is keeping record-keeping current (example).
  • New Release (v1.1.19): A new tagged release pushed in October (details).

🛠️ DevOps and Build

  • Executable Names: Several executables were renamed in CMakeLists.txt for clarity and maintainability.
  • Workflow Actions: Github workflow actions were temporarily disabled, perhaps to triage stability or build issues.

🧩 Merge Activity and Collaboration

  • Numerous merges of branches and remote-tracking branches signal active collaboration.
  • Community developers, such as Jakub Smulski, have contributed via merges.

🧼 Miscellaneous

  • .gitignore: Removed at one point, possibly as part of project clean-up.
  • GMM Files: Gaussian mixture model files added to the repository, prefiguring future map/model processing features, although not yet integrated into the build (details).
  • Parser and GUI: Added for GPhL BUSTER screen output and additional glycosylation debugging (details).

🚧 Note: This is only a partial summary

GitHub indicates there are 278 commits since October 2025, but only the first 30 could be programmatically summarized here. More detailed review and changes can be viewed directly in the commit history since October 2025.

Compiled December 2025