Bandicoot is a macOS-native fork of Coot 0.9.8.95, the structural biology macromolecular model-building program. It keeps Coot 0.9's functionality while replacing the UI elements that stop the app from functioning in MacOS Tahoe (26.x) on Apple Silicon, and adds some capabilities Coot 0.9 does not have.
RELEASES: Tarballs of binary releases are found at https://github.com/fraser-lab/bandicoot/releases
NOTE: Bandicoot targets macOS Tahoe (26.x) on Apple Silicon. It is not built or tested on other macOS releases, Linux, or Windows.
NOTE Bandicoot is a work in progress; users are welcome to log issues and issue pull requests.
The Crystallographic Object-Oriented Tool (Coot) has been the go-to suite of software for molecular modeling, used by thousands of structural biologists all over the world for over twenty years. Recently, Coot has been fully reimagined and redesigned, as well as giving the libraries and packages under the hood a much-needed upgrade. The resulting program (Coot 1) is in wide use today. However, many suites of software for structural biology rely on the old Coot 0.9 framework in order to function, making it necessary for both versions to remain in circulation.
While Coot 0.9.8.95 is distributed alongside Coot 1 in suites such as CCP4, it has become completely unusable on the most recent MacOS version (26.x, Tahoe). Bandicoot, a fork of Coot 0.9.8.95, addresses each of these with macOS-specific fixes layered on top of upstream Coot. See What changed vs Coot 0.9.8.95 below for a list of major changes.
The easiest way to install Bandicoot is to download a binary tarball (https://github.com/fraser-lab/bandicoot/releases) and install it (see INSTALL.md): untar it anywhere and launch <extracted>/bin/bcoot.
To build from source instead, see BUILD.md. You'll need a handful of Homebrew packages and a Miniconda environment that supplies Clipper, MMDB2, FFTW2, and a few others.
The changes fall into two categories: adjustments made to enable Coot 0.9 to run on MacOS 26.x Tahoe and features new in Bandicoot (or expanded from their Coot 0.9 versions).
(NOTE: Known problems and limitations are listed in OUTSTANDING_ISSUES.md).
- No XQuartz. freeglut is removed entirely, so nothing starts an X11 server.
- Menu bar. Coot's menu bar is mirrored into the system menu bar, and the in-window menu bar is hidden.
- Toolbars render outside the GL layer. The top toolbar is mirrored into a native toolbar on the window's title bar, and the vertical model toolbar is moved into its own window, because widgets over the GL backing layer do not draw.
- Docked panels are native. The docked Accept/Reject bar, sequence view and status bar are drawn as native panels over the content area. The GTK versions paint correctly into a buffer that is never composited, so they were invisible.
- Atom labels and axes use native text. The GLUT text paths that Coot 0.9 relies on are broken here and are bypassed.
- Retina-correct GL viewport and picking, so the framebuffer fills the window and a click picks the atom under the pointer rather than an offset one.
- Modifier keys are read from the window system directly, because GTK-Quartz does not report them to the application. Option-click acts as the middle mouse button on trackpads.
- Window behaviour. Dialogs float freely and raise reliably, windows open near the pointer, and external-monitor resolution is handled.
- Application identity. Native Dock icon and Dock Quit handling, a working Exit menu item, and the binary is named so the app menu and Dock show Bandicoot rather than a wrapper script.
- Python 3. A full replacement of the Python 2 elements of Coot 0.9 with Python 3 code.
- mmCIF handling rebuilt on gemmi. All mmCIF reading and writing goes through gemmi, with complete fidelity. The Header Browser shows real mmCIF metadata.
- CIF files are classified by content. Bandicoot now distinguishes coordinate vs. restraint mmCIF files if they are drag/dropped into the main window.
- More files open: modern small-molecule CIFs, and Phenix-produced CIFs can now be read in.
- Extended wwPDB identifiers. New-style entry IDs are fetched from the current archive. (Full compatibility with the new PDB archive will be implemented when that archive goes online in 2027.)
- Configurable atom-pick radii, separately for ordinary, symmetry and intermediate atoms.
- Live MolProbity probe dots preview. With "Interactive Dots" toggled on, moving atoms during real-space refinement previews clashes.
- "Modelling" is made into its own top menu item.
- "Glyco" is now an item in "Modelling". It is also always visible and accessible.
- Ctrl-C in the launching terminal shuts the program down.
Capabilities with no Coot 0.9 equivalent.
- Ligand restraints generation. Restraints are generated for unrecognised ligands on load, through an external generator, and stored per molecule. A dialog lists the components it can describe and lets you exclude any of them; it is also reachable from Modelling -> Generate Ligand Restraints.
- Colour by alternate conformation is now available as an option in the Display Manager; this scheme assigns different colors to residues in alternate conformations. It is now the default bond scheme, with preferences for the scheme itself and for how far the alternate conformers differ in colour from the bulk model.
- Session recording. An optional event log of a modelling session: where the user looked and what the maps showed there, every command Coot echoes, residue-level model edits, and clicks on validation results. Off unless asked for -- start it with
BANDICOOT_RECORD=1 bcootorstart_session_recording()in the scripting console. See SESSION_RECORDING.md. - PanDDA Inspect interface, with an HTML report, a
--pandda <dir>option and its own launcher. Can also be invoked by running<extracted>/bin/bandicoot.inspectwithin the panDDA folder itself. - Ligand from SMILES. Now an option in the Other Modelling Tools window.
- New Toolbar Buttons. Auto-open MTZ, Open Map and Quicksave.
- Bulk alternate-conformation rename from Residue Info. Allows assignment of an altloc code even if only a single alternate conformation exists. (E.g. when modeling a partially occupied water molecule that overlaps with a modeled alternate conformation of a nearby sidechain.)
Bandicoot inherits the GNU General Public License v3 from upstream Coot. The full text of the license is in COPYING.
The Bandicoot-specific patches are licensed under the same GPL v3 terms.
The binary tarball also bundles a number of third-party libraries, tools, and fonts distributed under their own (GPL-compatible) licenses. These are enumerated in THIRD_PARTY_LICENSES.md.
Bandicoot builds on the work of Paul Emsley, Bernhard Lohkamp, Kevin Cowtan, and the many other contributors to Coot. The macOS-native patches were developed by Art Lyubimov for use within the Fraser Lab at UCSF.
For the upstream Coot README, see README.coot.md.
This work was supported by Radial (ROR: https://ror.org/050rbg919) as part of the DiffUSE project.