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cryoDRGN
  • CryoDRGN User Guide
    • News and Release Notes
  • Installation
  • CryoDRGN EMPIAR-10076 Tutorial
  • CryoDRGN2 Ab Initio Reconstruction
  • CryoDRGN-ET Subtomogram Analysis
  • CryoDRGN Conformational Landscape Analysis
  • Making long trajectories with cryoDRGN graph_traversal
  • FAQ & Troubleshooting
  • Helpful Resources
    • ChimeraX tips
  • Deprecated Workflows
    • Handling large datasets with cryoDRGN preprocess
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  • CryoDRGN Tips
  • Chimerax
  • Useful Links

Helpful Resources

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Last updated 11 months ago

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

Useful Links

  • Anaconda:

  • Jupyter notebooks:

  • Setting up jupyter notebooks remotely:

ChimeraX tips
https://docs.anaconda.com/free/anaconda/install/
https://jupyter.readthedocs.io/en/latest/running.html
https://docs.anaconda.com/anaconda/user-guide/tasks/remote-jupyter-notebook/