PyMOL Claude MCP
Small Python stdio MCP bridge between Claude Code and a live PyMOL session over PyMOLs XML-RPC server. It exposes tools to run PyMOL commands, execute Python scripts inside PyMOL, and query XML-RPC methods for structure fetches, selections, representations, coloring, measurements, and atom or chain lookups. Public GitHub repository created September 2, 2026.
MCP unverified
Integration
| Transport | stdio |
| Auth | none |
| Endpoint | python pymol_server.py |
| Install | git clone https://github.com/stavasol96-arch/Pymol-Claude-MCP.git && cd Pymol-Claude-MCP && python3 -m venv venv && source venv/bin/activate && pip install -r requirements.txt |
Use Cases
| 01 | Drive an already-running PyMOL session from Claude Code or another MCP-compatible client |
| 02 | Fetch molecular structures, create selections, adjust representations, color scenes, and measure distances |
| 03 | Run PyMOL commands or scripts from an agent while keeping PyMOL local on the users machine |
Tags
pymol molecular-visualization proteins xml-rpc chemistry biology python claude-code
Machine-readable: /api/servers.json
· JSON-LD schema embedded in <head>