CryoDRGN-ET subtomogram analysis

Heterogeneous reconstruction of cryo-ET subtomograms

Now available in production/stable release in cryodrgn version 3.3.0! See News and release notes

CryoDRGN-ET is available in version 3.0.0+ through the same cryodrgn software interface with additional flags for subtomogram analysis. See our preprint here for a description of cryoDRGN-ET and associated results.

Preprocessing

Currently, cryoDRGN-ET expects 2D particle tilt series images in a .star file that is exported from Warp/M or RELION5.

1. Downsample images

(cryodrgn) $ cryodrgn downsample particles_from_M.star --datadir particleseries -D 128 -o particleseries/128.mrcs

2. Parse pose information

(cryodrgn) $ cryodrgn parse_pose_star particles_from_M.star -o pose.pkl -D 294 --Apix 1.7 

3. Parse CTF information

(cryodrgn) $ cryodrgn parse_ctf_star particles_from_M.star -o ctf.pkl -D 294 --Apix 1.7 

4. Test inputs are correctly parsed with traditional homogeneous reconstruction (GPU required)

(cryodrgn) $ cryodrgn backproject_voxel particles_from_M.star --datadir particleseries/128 --ctf ctf.pkl --poses pose.pkl --dose-per-tilt 2.93 -o reconstruct.mrc

CryoDRGN-ET training

Example command:

(cryodrgn) $ cryodrgn train_vae particles_from_M.star --ctf ctf.pkl --poses pose.pkl --datadir path/to/particle/subtilts --encode-mode tilt --dose-per-tilt 2.93 --zdim 8 -n 50 --beta .025 -o output_directory 

In particular:

• --encode-mode tilt is required to properly treat tilt series data

• --dose-per-tilt and --angle-per-tilt are used for dose exposure correction. The default value of --angle-per-tilt is 3 degrees and is left off of the example command.

• In our current experiments, we use a KL regularization weight of --beta 0.025

Training a model on 16,655 particles for 50 epochs on 1 A100 GPU took 3h, 38min.

Analysis

Once a cryoDRGN-ET model has finished training, use cryodrgn analyze to visualize the latent space and generate volumes.

(cryodrgn) $ cryodrgn analyze output_directory 49 # or replace with a different epoch number

This portion of the analysis is similar to the workflow in single particle cryodrgn. See the EMPIAR-10076 tutorial for further documentation.

Feedback

Please file a github issue or contact Ellen ([e-mail]) with any questions or feedback!