Python wrappers for CryoEM/CryoET programs that can be executed from the command line. The wrappers have been designed to be compatible with the definition of external jobs in Relion. They have only two arguments: input JSON values with key=value pairs and the output folder.
pip install emwrapOr for development:
git clone [email protected]:3dem/emwrap.git
pip install -e emwrap/| Job | Description | Commands | Packages |
|---|---|---|---|
| emw-import-ts | Import raw frames and MDOC files | emwrap | |
| emw-warp-mctf | Warp's motion correction and CTF | create_settings, fs_motion_and_ctf | Warp |
| emw-warp-aretomo | Tilt series alignment with Aretomo through Warp's wrapper. | ts_import, create_settings, ts_aretomo | Warp, AreTomo2 |
| emw-warp-ctfrec | Warp 3D CTF and reconstruction | ts_ctf, ts_reconstruct | Warp |
| emw-warp-pytom | Particle picking by template matching | pytom_match_pick, pytom_extract | PyTOM |
| emw-relion-tomorecons | Reconstruct an initial volume from input sub-tomograms | WORK-IN-PROGRESS | Relion |
| emw-relion-tomorefine | 3D Refine sub-tomogram particles | WORK-IN-PROGRESS | Relion |