# cryoDRGN

## cryoDRGN

- [CryoDRGN User Guide](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-user-guide.md): Welcome to cryoDRGN's documentation!
- [News and Release Notes](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-user-guide/news-and-release-notes.md): a timeline of updates to cryoDRGN
- [Installation](https://ez-lab.gitbook.io/cryodrgn/installation.md): instructions for installing cryoDRGN
- [CryoDRGN EMPIAR-10076 Tutorial](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-empiar-10076-tutorial.md): step-by-step tutorial on reconstruction with the assembling ribosome dataset using cryoDRGN
- [CryoDRGN-AI ab initio reconstruction](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-ai-ab-initio-reconstruction.md): how to use the command \<cryodrgn abinit>
- [Running reconstruction experiments](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-ai-ab-initio-reconstruction/running-reconstruction-experiments.md): executing and analyzing a particle reconstruction model with cryoDRGN-AI
- [CryoDRGN-AI ab initio EMPIAR-10076 tutorial](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-ai-ab-initio-reconstruction/cryodrgn-ai-ab-initio-empiar-10076-tutorial.md): ab initio reconstruction with the 50S dataset using cryoDRGN-AI volume reconstruction
- [cryodrgn abinit command API](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-ai-ab-initio-reconstruction/cryodrgn-abinit-command-api.md): full list of parameters that can be used to control the behavior of the cryodrgn abinit command
- [CryoDRGN-ET Subtomogram Analysis](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-et-subtomogram-analysis.md): how to perform heterogeneous reconstruction using cryo-ET subtomograms
- [CryoDRGN Conformational Landscape Analysis](https://ez-lab.gitbook.io/cryodrgn/cryodrgn-conformational-landscape-analysis.md): applying the cryodrgn analyze\_landscape commands to better understand a model's latent z-space
- [Making long trajectories with cryoDRGN graph\_traversal](https://ez-lab.gitbook.io/cryodrgn/making-long-trajectories-with-cryodrgn-graph_traversal.md): using cryoDRGN's tool for creating nearest-neighbor paths in the latent z-space
- [FAQ & Troubleshooting](https://ez-lab.gitbook.io/cryodrgn/faq-and-troubleshooting.md): (Work in progress)
- [Helpful Resources](https://ez-lab.gitbook.io/cryodrgn/helpful-resources.md): (Work in progress)
- [ChimeraX tips](https://ez-lab.gitbook.io/cryodrgn/helpful-resources/chimerax-tips.md)
- [CryoDRGN2 Ab Initio Reconstruction](https://ez-lab.gitbook.io/cryodrgn/deprecated-workflows/cryodrgn2-ab-initio-reconstruction.md): how to use the commands cryodrgn abinit\_homo and crydrgn abinit\_het
- [Handling large datasets with cryoDRGN preprocess](https://ez-lab.gitbook.io/cryodrgn/deprecated-workflows/handling-large-datasets-with-cryodrgn-preprocess.md): making bulky datasets fit into memory for model training