PyMOL MCP Connector

Example Use Cases

• 1

  Load, render, and manipulate PDB structures in PyMOL using natural language commands.

• 2

  Change representations, colors, and camera views programmatically to create publication-quality visualizations.

• 3

  Perform structural analyses (distances, alignments, residue highlighting) or execute arbitrary Python within PyMOL from an AI assistant.

Description

PyMOL-MCP links PyMOL with Claude Desktop using the Model Context Protocol so Claude can send commands, run Python code, and control PyMOL interactively. It supports loading PDBs, changing representations and colors, performing structural analyses (distances, alignments), and saving high-resolution images. The project is distributed as a PyMOL plugin and a Python MCP server script for local two-way communication between PyMOL and Claude.