pymol-fundamentals

What problem does it solve?

PyMOL workflows can be tedious to coordinate: loading structures, creating representations, applying colors, making selections, and performing measurements across single or multiple structures.

Core Features & Use Cases

• Load structures from PDB or local files via the pymol-agent-bridge
• Create and switch representations (cartoon, sticks, surfaces) and apply color schemes
• Make selections, run measurements, and perform quick analyses for exploratory visualization
• Use case: researchers visualize a protein and its ligand, then measure distances and angles to assess binding geometry

Quick Start

Ask Claude to run the pymol-setup flow and load a structure to begin visualizing in PyMOL.