Heterogeneity (tomoDRGN)¶

nextPYP supports running tomoDRGN on existing tomography projects

Requirements¶

• An existing Particle refinement block with a succesful consensus refinement

• Access to a GPU

tomoDRGN workflow¶

nextPYP follows the general protocol described in the tomoDRGN documentation

Preparation¶

1. Since tomoDRGN uses particle projections extracted from the tilt-series data, we first need to generate these particles stacks. This is done in the Particle refinement block, by going to the Extraction tab and selecting the option Save particle stacks

2. Click Save, Run, and Start Run for 1 block

Learn structural heterogeneity¶

Once the particle stacks have been generated, we can proceed to run tomDRGN:

1. Click on Particles (output of the Particle refinement block) and select tomoDRGN (train-vae)

2. Select the Input file (*.star) by navigating to the stacks directory in the default location from the upstream block and selecting the file *_particles.star

3. Adjust tomoDRGN parameters as needed according to the Command Usage instructions

4. Click Save, Run, and Start Run for 1 block. This will run tomoDRGN’s train-vae and convergence-vae commands

5. Check the results by navigating to the tomoDRGN (train-vae) block

Analyze structural heterogeneity (analyze)¶

The next step is to analyze the results using standard latent space analysis:

1. Click on DRGN Model (output of the tomoDRGN (train-vae) block) and select tomoDRGN (analyze)

2. Adjust any tomoDRGN parameters as needed according to the Command Usage instructions

3. Click Save, Run, and Start Run for 1 block. This will run tomoDRGN’s analyze command

4. Check the results by navigating to the tomoDRGN (analyze) block

Analyze structural heterogeneity (analyze-volumes)¶

Results can also be analyzed using standard volume space analysis:

1. Click on DRGN Model (output of the tomoDRGN (train-vae) block) and select tomoDRGN (analyze-volumes)

2. Adjust any tomoDRGN parameters as needed according to the Command Usage instructions

3. Click Save, Run, and Start Run for 1 block. This will run tomoDRGN’s analyze-volumes command

4. Check the results by navigating to the tomoDRGN (analyze-volumes) block

Select particle subsets (filter-star)¶

1. Click on DRGN Particles (output of the tomoDRGN (analyze) or tomoDRGN (analyze-volumes) blocks) and select tomoDRGN (filter-star)

2. Select the classes you want to keep as a comma separated list

3. Click Save, Run, and Start Run for 1 block. This will run tomoDRGN’s filter-star command

Further refine selected particles¶

1. Click on Particles (output of the tomoDRGN (filter-star) block) and select Particle refinement

2. Set the neccesary parameters

3. Click Save, Run, and Start Run for 1 block

4. Check the results by navigating to the Particle refinement block