# 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


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on a page URL with the `ask` query parameter:
```
GET https://ez-lab.gitbook.io/cryodrgn/cryodrgn-user-guide.md?ask=<question>
```
The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.