Scripts to facilitate STA, interfacing Warp/M, Relion 3.1, TomoTwin and whatever else seems relevant.
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.
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.
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.
- (Optional) create a fresh mamba/conda environment with Python >= 3.8:
mamba create -n subtomotools python=3.8 -c conda-forge
- Install
subtomotools
from pip viapip install "git+https://github.com/tomotools/subtomotools.git"
- Call the indiviudal programs directly from the command line and use
--help
to see options, e.g.dedup-3d --help