Bandicoot

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 full functionality while changing several UI elements in order for the app to function in MacOS Tahoe (26.x) on Apple Silicon.

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.

Why a fork?

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 (2.6x, 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 the end of this document for a list of major changes from Coot 0.9.8.95.

Quick start

If you have a prebuilt binary tarball (bandicoot-0.0.0.1-darwin-arm64.tar.gz), 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.

What changed vs Coot 0.9.8.95

• Native macOS menu bar. Coot's GtkMenuBar is walked at startup and mirrored into the system menu bar via [NSApp setMainMenu:]. The in-window menu bar widget is hidden.
• Native macOS toolbar. Coot's top main_toolbar is mirrored into an NSToolbar (with icons extracted from each GtkToolButton's GtkImage) and attached to the main NSWindow's title bar. An "Auto-open MTZ" item is added next to "Open Coords...".
• Floating model toolbar. The vertical side toolbar (model_toolbar) is reparented into its own GtkWindow (transient to the main window), so its widgets render outside the GL backing layer's territory. The toolbar's customization popup (icons / text / both) still works thanks to a support.c::lookup_widget patch that consults a GladeParentKey data pointer on reparented toplevels.
• Native text rendering for atom labels and axes. The broken GLUT text paths are bypassed; instead, labels are rendered with NSString drawAtPoint into an NSBitmapImageRep, uploaded as a GL texture, and drawn as a textured quad in the same matrix transform Coot's existing label code uses. Font is Menlo (monospace), size driven by Coot's atom_label_font_size preference.
• Retina-correct GL viewport and atom picking. glViewport and gluUnProject multiply by [NSScreen backingScaleFactor], so the GL framebuffer fills the contentView and clicks pick the right atom.
• Modifier keys via AppKit. [NSEvent modifierFlags] is queried directly in glarea_button_press (and any caller of bandicoot_shift_pressed / bandicoot_control_pressed) because GTK-Quartz on Tahoe never populates event->state with modifier bits.
• Click deduplication. Button-press events arriving within 100 ms of the previous one on the same button are dropped, so the multi-event burst Tahoe generates for a single physical click doesn't fire toggle handlers multiple times.
• App activation, splash screen, and identification. On launch the app calls [NSApp activateIgnoringOtherApps:] so its windows come to the foreground; the Bandicoot splash PNG is shown for a guaranteed 2.5 s before the main window appears; the title bar reads "Bandicoot (Coot 0.9.8.95, built <date>)".

The executable on disk is called bcoot (a symlink to the existing coot wrapper script).

License

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.

Credits

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.

Funding

This work was supported by Radial (ROR: https://ror.org/050rbg919) as part of the DiffUSE project.