Use when working with PyMOL for molecular visualization tasks including loading structures, creating representations, coloring, selections, and basic analysis.
Use when connecting Claude to PyMOL, troubleshooting socket errors, or setting up the PyMOL integration for the first time
Use when setting up, configuring, running, or inspecting La-Proteina protein generation tasks including unconditional design and motif scaffolding. Helps build configs and visualize outputs through PyMOL.
Use when setting up, configuring, running, or inspecting Proteina-Complexa protein binder design, ligand binder design, AME motif scaffolding, or monomer motif scaffolding. Helps build configs, select targets, and visualize outputs through PyMOL.
Use when validating protein designs with AlphaFold2/AlphaFold3/ESMFold predictions, coloring by pLDDT or pAE, computing self-consistency RMSD, or screening design candidates through PyMOL.
Use when comparing multiple protein designs, ranking design candidates, tracking design iterations, overlaying before/after structures, or performing batch visual QC through PyMOL.
Use when analyzing protein-protein or protein-ligand interfaces in designed complexes, computing buried surface area, identifying hotspot contacts, or characterizing binding interfaces through PyMOL.
Use when visualizing ProteinMPNN or LigandMPNN sequence design results, inspecting designed vs. fixed residues, viewing per-position confidence, or analyzing sequence design outputs through PyMOL.