Simulate ribosomes' micrographs with the TEM simulator

[ninamiolane]

What?

• Run tem_tutorial.ipynb in a docker container.
• Get the PDB file (see section "How?") that represents your atomic model, serving as basis for the simulation
• Adapt the code in the tem_tutorial.ipynb to simulate from your PDB file.
• Upload your micrographs to the OSF folder simSPI.

Notes:

• This task requires using a docker container to run the TEM simulator.
• This task is related to tasks:
  • Simulate Gaba-B proteins' micrographs with the TEM simulator #108
  • Simulate spliceosomes' micrographs with the TEM simulator #110 .

Why?

Micrographs are arguably the most important type data of raw cryo-EM data.

Being able to simulate micrographs easily is fundamental to rapidly test novel reconstruction methods in cryo-EM.

Where?

• Your simulation notebook should go in the notebooks folder.

How?

Get PDB files from these three atomic structures:

• Download CIF file for the atomic structure:
  • Bacterial Ribosome at 2 Angstrom Resolution
• Use ioSPI/atomic_models.py module to convert it into a PDB file.

Upload the resulting micrographs to OSF simSPI project:

• Follow the steps in the notebooks download_and_upload_with_osf.ipynb