CryoDRGN is an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It contains interactive tools to visualize a dataset’s distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions. CryoDRGN is open-source software freely available at http://cryodrgn.csail.mit.edu.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --gres=gpu:k80:1 [user@cn4199 ~]$ module load cryoDRGN [+] Loading singularity 3.8.5-1 on cn4199 [+] Loading cryoDRGN 1.1.0 ...Copy test data to your current folder:
[user@user@cn4199 ~]$ cp -r $CRYODRGN_TEST/* .Downsample test data:
[user@cn4199 ~]$ cryodrgn -h
usage: cryodrgn [-h] [--version]
{preprocess,downsample,parse_pose_csparc,parse_pose_star,parse_ctf_csparc,parse_ctf_star,train_nn,backproject_voxel,train_vae,eval_vol,eval_images,analyze,analyze_landscape,analyze_landscape_full,pc_traversal,graph_traversal,view_config}
...
CryoDRGN neural network reconstruction
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
Choose a command:
{preprocess,downsample,parse_pose_csparc,parse_pose_star,parse_ctf_csparc,parse_ctf_star,train_nn,backproject_voxel,train_vae,eval_vol,eval_images,analyze,analyze_landscape,analyze_landscape_full,pc_traversal,graph_traversal,view_config}
[user@cn4199 ~]$ cryodrgn downsample -h
usage: cryodrgn downsample [-h] -D D -o MRCS [-b B] [--is-vol] [--chunk CHUNK]
[--datadir DATADIR] [--max-threads MAX_THREADS]
mrcs
Downsample an image stack or volume by clipping fourier frequencies
positional arguments:
mrcs Input particles or volume (.mrc, .mrcs, .star, or
.txt)
optional arguments:
-h, --help show this help message and exit
-D D New box size in pixels, must be even
-o MRCS Output projection stack (.mrcs)
-b B Batch size for processing images (default: 5000)
--is-vol Flag if input .mrc is a volume
--chunk CHUNK Chunksize (in # of images) to split particle stack
when saving
--datadir DATADIR Optionally provide path to input .mrcs if loading from
a .star or .cs file
--max-threads MAX_THREADS
Maximum number of CPU cores for parallelization
(default: 16)
[user@cn4199 ~]$ cryodrgn downsample data/toy_projections.mrcs -D 24 -o particles.24.mrcs
2022-09-08 12:24:55 Processing batch 0
2022-09-08 12:24:55 (1000, 24, 24)
2022-09-08 12:24:55 Saving /gpfs/gsfs7/users/user/cryoDRGN/particles.24.mrcs
Parse image poses from a consensus homogeneous reconstruction:
[user@cn4199 ~]$ cryodrgn parse_pose_star -h
usage: cryodrgn parse_pose_star [-h] -o PKL [-D D] [--Apix APIX] input
Parse image poses from RELION .star file
positional arguments:
input RELION .star file
optional arguments:
-h, --help show this help message and exit
-o PKL Output pose.pkl
Optionally provide missing image parameters:
-D D Box size of reconstruction (pixels)
--Apix APIX Pixel size (A); Required if translations are specified in
Angstroms
[user@cn4199 ~]$ cryodrgn parse_pose_star data/relion31.star -o test.pkl -D 300 --Apix 1.03
2022-09-08 12:26:14 5 particles
2022-09-08 12:26:14 Euler angles (Rot, Tilt, Psi):
2022-09-08 12:26:14 [-102.30296 82.318041 124.706463]
2022-09-08 12:26:14 Converting to rotation matrix:
2022-09-08 12:26:14 [[ 0.81941806 -0.10080704 0.56426234]
[-0.53288075 0.22868946 0.81470193]
[-0.21116853 -0.96826601 0.13367414]]
2022-09-08 12:26:14 Translations (pixels):
2022-09-08 12:26:14 [ 0.00688667 -0.23052744]
2022-09-08 12:26:14 Writing /gpfs/gsfs7/users/user/cryoDRGN/test.pkl
Parse CTF parameters from a .star/.cs file:
[user@cn4199 ~]$ cryodrgn parse_ctf_star -h
usage: cryodrgn parse_ctf_star [-h] -o O [--png PNG] [-D D] [--Apix APIX]
[--kv KV] [--cs CS] [-w W] [--ps PS]
star
Parse CTF parameters from a RELION .star file
positional arguments:
star Input
optional arguments:
-h, --help show this help message and exit
-o O Output pkl of CTF parameters
--png PNG Optionally plot the CTF
Optionally provide missing image parameters:
-D D Image size in pixels
--Apix APIX Angstroms per pixel
--kv KV Accelerating voltage (kV)
--cs CS Spherical abberation (mm)
-w W Amplitude contrast ratio
--ps PS Phase shift (deg)
[user@cn4199 ~]$ cryodrgn parse_ctf_star data/relion31.star -D 300 --Apix 1.03 -o ctf.pkl --relio
n31 --kv 10 --cs 1 -w 0.5
2021-02-24 10:24:39 5 particles
2021-02-24 10:24:39 Overriding accerlating voltage with 10.0 kV
2021-02-24 10:24:39 Overriding spherical abberation with 1.0 mm
2021-02-24 10:24:39 Overriding amplitude contrast ratio with 0.5
2021-02-24 10:24:39 CTF parameters for first particle:
2021-02-24 10:24:39 Image size (pix) : 300
2021-02-24 10:24:39 A/pix : 1.03
2021-02-24 10:24:39 DefocusU (A) : 13108.082418
2021-02-24 10:24:39 DefocusV (A) : 12845.582418
2021-02-24 10:24:39 Dfang (deg) : -160.39
2021-02-24 10:24:39 voltage (kV) : 10.0
2021-02-24 10:24:39 cs (mm) : 1.0
2021-02-24 10:24:39 w : 0.5
2021-02-24 10:24:39 Phase shift (deg) : 0.0
2021-02-24 10:24:39 Saving ctf.pkl
[user@cn4199 ~]$ cryodrgn downsample data/relion31.star -D 24 -o relion31.24.mrcs
2022-09-08 12:33:30 Processing batch 0
2022-09-08 12:33:30 (5, 24, 24)
2022-09-08 12:33:30 Saving /gpfs/gsfs7/users/user/cryoDRGN/relion31.24.mrcs
[user@cn4199 ~]$ exit
salloc.exe: Relinquishing job allocation 59748321
[user@biowulf ~]$
Create a batch input file (e.g. CryoDRGN.sh). For example:
#!/bin/bash module load CryoDRGN cp -r $CRYODRGN_TEST/* . cryodrgn parse_pose_star data/relion31.star -o test.pkl -D 300 --Apix 1.03 cryodrgn parse_ctf_star data/relion31.star -D 300 --Apix 1.03 -o ctf.pkl --kv 10 --cs 1 -w 0.5
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] CryoDRGN.sh