It drives the PyMOL session you already have open rather than a headless copy, so what the model does shows up on your screen — and the arbitrary-Python path means it is not limited to the operations someone thought to wrap.
A socket bridge between Claude and PyMOL. A PyMOL plugin listens on port 9876 and the MCP server connects to it, so a request in the chat becomes a command in the PyMOL session already open in front of you.
- Molecular visualization driven in plain language — representations, colours and views
- Structural analysis: measurements, alignments and comparisons between structures
- Arbitrary Python executed inside PyMOL when a task needs more than a command
- Two-way communication over the socket, so PyMOL's own output comes back rather than disappearing
- Natural-language parsing of PyMOL commands, so "colour by secondary structure" does not have to be translated first
PyMOL, Claude for Desktop, Python 3.10 or newer, and Git. Install the plugin from `pymol-mcp-socket-plugin/__init__.py` through PyMOL's Plugin Manager, then click Start Listening and check the status reads "Listening on port 9876". The socket is local: PyMOL and Claude must be on the same machine. MIT.
One command — [Full path to your venv python] [Full path to pymol_mcp_server.py]