A Moorhen fork that quacks like a Coot.

PyKeko is a macOS desktop application for the interactive macromolecular visualization and model building of structures determined by X-ray crystallography and cryo-EM.

Under the hood it is Moorhen, Coot's C++ engine (libcootapi, CCP4, Clipper, MMDB, GEMMI, RDKit) compiled to WebAssembly and wrapped in a TypeScript/React interface. PyKeko packages that into a self-contained, one-click .app/.dmg and tunes it to feel like Coot 0.9.x - with similar keyboard shortcuts, defaults, and workflow primitives — while adding features of its own: a PyMOL command-language scripting console and a PyMOL--R-style RPC server, command-line integration, a residue torsion editor, Claude-MCP control, and more.

PyKeko is an independent project not affiliated with or endorsed by the Moorhen or Coot teams — but built on their extensive work (see Credits).

Coot 0.9.x renders through XQuartz/GLX, which does not work on recent macOS versions (Tahoe done broke it). PyKeko requires no XQuartz and no compiler — download the .dmg and go. CCP4 is optional: the core build / refine / save workflow is bundled, but if you do have CCP4 installed PyKeko transparently picks up its acedrg, findligand, and refmac5 binaries for a handful of advanced features (SMILES → CIF dict fallback, ligand-site search, in-app REFMAC5 refinement of covalent links). A lot of crystallographers miss the the feel of pre-v1.0 Coot...

⬇ Download the latest PyKeko.dmg · Full install guide

1. Open the DMG and drag PyKeko to your Applications folder.
2. First launch (the build is unsigned): right-click the app → Open, or run xattr -dr com.apple.quarantine /Applications/PyKeko.app.

Already on an earlier version? See upgrading — your settings and the pykeko command-line tool carry over.

Requires macOS 15.x (Tahoe) on Apple Silicon. The core app — Electron, the WebAssembly Coot engine, the monomer libraries — is fully bundled and works offline (except "Fetch from PDB").

CCP4 is optional. When CCP4 is installed (/Applications/ccp4-9/ or on PATH) PyKeko transparently shells out to:

Without CCP4 those specific menu items become no-ops with a "CCP4 not installed" message; everything else in PyKeko works.

A rolling snapshot of the bigger additions across the 0.2.x → 0.3 line. Full per-release notes →

• PyMOL-style selection algebra — byres polymer within 5 of organic, chain A and resi 100-200, (b > 50) and polymer, chemical-class predicates, set algebra, within R of distance predicate. Edit → Selections… lets you evaluate an expression with a live count, then save it under a name (e.g. pocket) — saved selections persist across launches and .pykeko session files, and the PyMOL translator picks them up so color magenta, pocket works in any in-app PyMOL command.
• Interaction overlays — View → Interactions… detects + draws H-bonds (yellow dashed), salt bridges (blue), disulfides (gold), and clashes (hot-pink), each toggleable independently. Optional selection scope so e.g. detection runs only inside the binding pocket.
• Symmetry mates + unit cell box — View → Symmetry… reads the spacegroup + cell from the loaded structure and draws sym mate Cα traces within a radius slider of the rotation centre, in distinct colours per operator. Answers "is this density a sym-mate side chain?" and "is my binding mode a crystal-contact artefact?".
• Quick view chips — View → Quick views… for the daily-driver recipes: hide solvent / hide hydrogens / show only pocket / reset. Each fires a PyMOL command through the in-app translator.
• macOS ⌘Z / ⌘⇧Z for undo/redo (was Ctrl-Z only — broke Mac muscle memory), with Edit → Undo/Redo menu entries.
• PyMOL-style trackball rotation — Moorhen's Eulerian rotation (horizontal=yaw, vertical=pitch, no roll) replaced as default with a line-for-line port of PyMOL's Shoemake virtual trackball using the same constants (mouse_scale=1.3, mouse_limit=100, radius 0.45×min(W,H)). Feels like spinning a ball with your fingers, with natural edge-roll. Preferences → Mouse sensitivity… toggle to switch back to the Coot/Moorhen gimbal feel if you want it.
• DIMPLE auto-pipeline — new Ligand → Refine with DIMPLE… wraps CCP4's dimple (rigid-body / MR + restrained refinement + optional ligand fitting end-to-end). Load apo model, optionally a ligand from SMILES, click → pick MTZ → dimple runs in the background (typical 2–10 min, progress in the in-app log console) → refined model loads back automatically.
• In-app log console + scripting REPL — a thin always-on strip at the bottom of the viewport tails PyKeko's log so you can see what the app is doing without dropping to Terminal. ⌘` expands it into a scrollable panel with filter + colour-coded levels, plus a REPL with a JS / PyMOL mode dropdown. The ! prefix runs the input through your login shell with ~/.zshrc sourced (so conda init, CCP4 setup, custom PATH all work); !cd, !pushd/!popd, !export, and !clear mutate process-wide state so subsequent saves and spawn helpers (refmac5 / findligand / acedrg) honour them.
• Covalent-ligand workflow + in-app REFMAC5 — Ligand → Make covalent…: pick a Cys SG and a ligand Cβ; PyKeko auto-detects the warhead family (acrylamide / α,β-ynamide / chloroacetamide / epoxide / maleimide / Mike-acceptor-vinyl), declares the link, and updates the displayed bond orders to match the post-reaction state. With CCP4 installed, one more click refines the model against your MTZ via the system's refmac5. Ligand → Find ligand sites… likewise drives CCP4's findligand to search Fo-Fc for ligand-shaped blobs.
• Real desktop session save/restore — File → Save session… writes a single .pykeko file (full scene: molecules, maps, per-rep colour rules, camera, vectors, 2D overlays, view settings); Open session… rehydrates it. Drag-drop onto the window also works.
• Portable Mol* viewer export — File → Export portable viewer (.html) produces a single self-contained HTML file (Mol* under the hood) that reproduces your visible scene (representations, colour rules, ligand spheres, density …) for sharing or embedding. Optional density map embedding gives a "rolling cube" that tracks the recipient's camera, à la Coot.
• Shell-style scripting history — Calculate → Interactive scripting's modal now has per-mode ↑/↓ history, Cmd/Ctrl+Enter to submit, and persistence across reloads. Works for both PyMOL and JavaScript modes.
• Command-line integration — pykeko model.pdb data.mtz ligand.cif opens files (the .cif attaching as a dictionary, not spawning a new molecule); pykeko 7sj3 fetches by PDB id; pykeko script.pml runs a PyMOL-style script. A second launch of pykeko hands its files to the running window (PyMOL -R style); --new opens a fresh one. Install the command from Preferences → Install command-line launcher.
• Residue torsion editor — right-click a residue → Edit torsions: rotate φ/ψ/χ angles with a live Ramachandran plot tracking the sliders.
• pykeko_remote.py — a PyMOL--R-style Python client that drives a running PyKeko from your own scripts (load / refine / screenshot / run PyMOL commands / …).
• Coot-style defaults — black background, hydrogens shown when present, PyMOL as the default scripting language. Updated keyboard shortcuts shown with 'm'.

Model building (inherited from Coot, via Moorhen). Real-space refinement (single → triple → sphere → chain → all), rotamer fitting, peptide flips, mutations, add/delete of atoms and residues, terminal-residue building, jiggle fit, ligand fitting, map manipulation and contouring, geometry/validation analysis, and reading/writing PDB, mmCIF, MTZ, and CCP4/MRC maps — all locally, no server.

Added by PyKeko on top of Moorhen:

Full keyboard-shortcut table and per-feature writeups: Moorhen-PyKeko/README-MH.md · PyMOL command reference: docs/pymol-translator.md.

Brief map below — each repo's own README goes in-depth on its internals.

PyKeko exists only because of the work it builds on:

• Moorhen — the Moorhen team's WebAssembly port of Coot and its React UI. PyKeko is a fork of their project, under their BSD-3-Clause license.
• Coot — Paul Emsley and the Coot developers (MRC-LMB), the original program this whole lineage descends from.
• CCP4, Clipper, MMDB, GEMMI, RDKit, and the other libraries Moorhen compiles to WebAssembly.

Licenses: PyKeko and PyKekoMCP are MIT; Moorhen-PyKeko follows upstream Moorhen's BSD-3-Clause license. See each repo's LICENSE.