Tutorials¶

The maintained examples now live in the repository-level tutorials/ folder. The legacy notebooks that previously lived under website/source/ are no longer the supported examples.

Core modeling tutorials¶

• quick_start_6bno.ipynb: shortest path from structure input to generated NERDSS files.
• ionerdss_tutorial_5l93.ipynb: structure processing and exported visualization outputs for 5l93.
• ionerdss_tutorial_6bno.ipynb: PDB-to-model workflow with ODE outputs and NERDSS-ready files.
• ionerdss_dodecahedron_tutorial.ipynb: platonic-solid workflow for generating a dodecahedron-based assembly.

Validation and advanced workflow tutorials¶

• ionerdss_tutorial_pdb_validation.ipynb: structure-validation workflow for comparing an assembled result against the designed coarse-grained target.
• ionerdss_tutorial_with_proaffinity_8y7s.ipynb: ProAffinity-enabled workflow for binding-affinity prediction on a larger assembly.
• ionerdss_tutorial_simularium.ipynb: convert NERDSS trajectories into the Simularium 3D viewer format.
• ionerdss_tutorial_ovito_gif.ipynb: render NERDSS trajectories into GIF animations using OVITO.

Additional examples¶

• additional_examples/4yd9.ipynb

Supplemental files in tutorials/¶

The tutorials folder also contains supporting outputs and helper files that are referenced by some notebooks:

• install_ADFR_mac.sh: helper script for installing the ADFR toolchain used by some ProAffinity workflows

Open locally¶

pip install -e ".[jupyter]"
jupyter lab tutorials/