subtomotools

Scripts to facilitate STA, interfacing Warp/M, Relion 3.1, TomoTwin and whatever else seems relevant.

Functions:

Star-file:

upgrade-star: Upgrade Warp-style star to Relion 3.1.4.
downgrade-star: Downgrade Relion-3-style star for Warp/M.
dedup-3d: Remove duplicate particles from star-file in 3D.

Particles:

project-particles: Calculate 2D projections of subtomograms, with or without CTF correction. CTF correction requires CTF volume.
apply-selection: Apply subset of particles from 2D classification to subtomogram star.

TomoTwin:

tomotwin2warp: Takes a folder of .coords files from TomoTwin, turns into star file based on prefix for subtomo reconstruction in Warp.
bash_helpers/*.sh: Bash-scripts to loop the steps of TomoTwin embedding and picking over many tomograms.

Installation:

1. (Optional) create a fresh mamba/conda environment with Python >= 3.8: mamba create -n subtomotools python=3.8 -c conda-forge
2. Install subtomotools from pip via pip install "git+https://github.com/tomotools/subtomotools.git"
3. Call the indiviudal programs directly from the command line and use --help to see options, e.g. dedup-3d --help