Helpful Resources

(Work in progress)

CryoDRGN Tips

• cryodrgn --version

• cryodrgn view_config [outdir]

  • As of version 2.3.0, you can also directly view the config.yaml file to see all parameters

• To optimize training speed, make sure the dimensions of the particle images and architecture settings (--zdim , --enc-dim , and --dec-dim ) are a multiple of 8.

Chimerax

ChimeraX tips

Useful Links

• Anaconda: https://docs.anaconda.com/free/anaconda/install/

• Jupyter notebooks: https://jupyter.readthedocs.io/en/latest/running.html

• Setting up jupyter notebooks remotely: https://docs.anaconda.com/anaconda/user-guide/tasks/remote-jupyter-notebook/