Agentic PyMOL MCP
An MCP server that links an agent to an open PyMOL: load structures, align, measure distances and render PNGs.
- 107 ★ on the repository
- Last commit
- MIT
Minimal access
Why this level
- The agent drives an open PyMOL session and can change objects and renders in it.
Install
- Works in
Manual install
Clone the repository and run `uv sync`, install `pymol_plugin/__init__.py` through Plugin Manager and click Start Listening, then register `.venv/bin/agentic-pymol` with `claude mcp add --scope user pymol`.
Access and checks
How we reviewMinimal accessThe tool runs nothing and makes no network calls.
- The agent drives an open PyMOL session and can change objects and renders in it.
This is third-party code. Review the repository files before installing.
What it does
Agentic PyMOL is a small bridge between a general-purpose agent and a PyMOL session you already have open. The agent drives the live session and gets data back as structures: objects, chains, coordinates, distances, RMSD, views, sequences and errors. It is not an embedded chat or a molecular workbench. Example tasks: fetch ubiquitin, show it as cartoon, color by secondary structure and save a PNG; build a table of residues in contact with DNA for structure `6EDC`; align chain A of two structures, report the RMSD and show regions that moved. Docking, sequence search, prediction and external biology APIs are deliberately left out. It connects to Claude Code, Claude Desktop, Codex CLI and VS Code Copilot.
Who it is for. Structural biologists and bioinformaticians who work in PyMOL and want to drive it in plain words through their own agent.
Good fit when
- Two structures need aligning with the moved regions shown at once.
- A table of contact residues is built from a protein-DNA structure.
- Ten binders are compared for a conformational shift of a loop.
- A paper needs a PNG render of a chosen view.
Not a fit when
- You need docking, sequence search or conservation analysis: the package leaves them out.
- PyMOL 3.1.0 on PyQt6 (Homebrew on macOS) is installed: the plugin crashes during install.
- A standalone chat inside PyMOL is needed.
Example request
Fetch ubiquitin, show it as cartoon, color by secondary structure and save the render as PNG.MCP
- Transport
- stdio
- Authentication
- not required
Limitations
PyMOL 2.6 or newer, the `uv` manager and an MCP client are required. The PyMOL plugin must be installed and started with "Start Listening". A PyMOL 3.1.0 build on PyQt6, such as the current Homebrew one on macOS, crashes while installing the plugin because of a bug in PyMOL itself. The server drives an open session, so the agent can change and close objects in it. Other PyMOL bridges exist, but this one returns typed data rather than just "succeeded".
How to disable. Stop listening in the PyMOL plugin menu, remove the plugin and run `claude mcp remove pymol` (or the equivalent for another client).
FAQ
How do I register it in Claude Code?
With `claude mcp add --scope user pymol /absolute/path/to/agentic-pymol/.venv/bin/agentic-pymol`, then verify with `claude mcp list`.
And in Codex CLI?
With `codex mcp add pymol -- /absolute/path/to/agentic-pymol/.venv/bin/agentic-pymol` and a check with `codex mcp list`.
Does PyMOL need a special launch?
No. The server works with your regular install; just enable listening in the plugin.
How does it differ from built-in chats?
The agent stays your general-purpose one, and PyMOL opens to it as typed tools with data read back.
Is there a setup video?
Yes, the README has a setup walkthrough video and a six-minute structure analysis demo.
Discussion
No questions or reviews yet.
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README in short
The README sets out the bridge, design goals, example prompts, install for four clients, usage and a comparison with other PyMOL projects.