Pymol-Claude-MCP

What it does

• Three tools cover the whole surface: pymol_command (any PyMOL command as typed), pymol_script (Python loops and cmd.* calls inside PyMOL), pymol_query (read-only lookups that return values)
• Wraps PyMOL's own XML-RPC server — no PyMOL fork or plugin needed; open-source PyMOL builds include it
• Optional autostart: symlink autostart/pymolrc.py to ~/.pymolrc.py so RPC starts silently on every PyMOL launch (port 9123, override with PYMOL_RPC_PORT or --port)
• Python 3.10+, standard venv install; registered into Claude Code with one claude mcp add

When to use it

Structural-biology work where you'd otherwise retype the same fetch/select/color/measure choreography: let Claude Code drive the session while you watch the viewport — preparing figures, exploring a new structure, or scripting repetitive analyses.

Getting started

git clone https://github.com/stavasol96-arch/Pymol-Claude-MCP
cd Pymol-Claude-MCP
python3 -m venv venv && source venv/bin/activate
pip install -r requirements.txt
ln -sf "$(pwd)/autostart/pymolrc.py" ~/.pymolrc.py   # optional RPC autostart
claude mcp add pymol $(pwd)/venv/bin/python3 $(pwd)/pymol_server.py

Start PyMOL (or pymol -R) before launching Claude Code, or the server fails to connect.

Things to know

PyMOL must already be running with RPC active before Claude Code starts. Niche audience (requires PyMOL and structural-biology context). No license file in the repo yet at review time.