chimerax-copick

A collaborative cryo-ET annotation plugin for ChimeraX.

Browse runs in a thumbnail gallery, load tomograms at any resolution, and create and edit particle picks, meshes, and segmentations — all stored in a portable copick project that works against local files, S3/SSH/SMB storage, or the CZ cryoET Data Portal. Picking and 3D visualization are powered by ArtiaX; volumes stream as multiscale OME-Zarr.

Installation

Install from the ChimeraX Toolshed: Tools → More Tools…, search for copick, click Install, and restart ChimeraX if prompted.

Requires ChimeraX ≥ 1.7. ArtiaX, ChimeraX-OME-Zarr, and copick are pulled in automatically.

To create or import projects from the command line (below), also install the copick CLI in your terminal environment:

pip install "copick[all]"

Quick start

A copick project is described by a small JSON config file. Point ChimeraX at one with copick start /path/to/config.json. Two ways to get a config in a couple of minutes:

From the CZ cryoET Data Portal (no downloads — objects and existing annotations are discovered automatically):

copick config dataportal --dataset-id 10301 --overlay ./overlay --output config.json

From your own MRC tomograms (local project):

# Create a local project and declare the objects you'll annotate
copick config filesystem \
    --config config.json \
    --overlay-root ./my_project \
    --objects ribosome,True,150,7P6Z --objects membrane,False \
    --proj-name my-project --proj-description "My cryo-ET dataset"

# Import tomograms (file type and voxel size are read from the MRC header)
copick add tomogram "tomograms/*.mrc" --config config.json --tomo-type wbp

Then, in the ChimeraX command line:

copick start config.json

Run cks to enable copick keyboard shortcuts, then press ? for the full list.

Documentation

• copick docs: https://copick.github.io/copick/
• ChimeraX-copick tutorial: https://copick.github.io/copick/examples/tutorials/chimerax/
• Quick start: https://copick.github.io/copick/quickstart/

OpenMoji attribution

Emoji glyphs on Linux are rendered with the bundled OpenMoji color font. All emojis are designed by OpenMoji and licensed under Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0). The full license text ships with the plugin at src/fonts/OpenMoji-LICENSE.txt.

License

MIT — see LICENSE.