Name: PyMOL-MCP
Author: vrtejus

LABSCO SUMMARY

Structural biology as a conversation.

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.

What it is

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.

What you get

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

Requirements

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.

Setup effort

Build from source — git clone https://github.com/vrtejus/pymol-mcp

See installation options

USE CASES

01

Loading and setting up a structure

Name the PDB entry and the representation you want, and it appears in the open session.

02

Highlighting the part you care about

Ask for the active-site residues as sticks, or colouring by secondary structure, in words rather than selectors.

03

Comparing two structures

Align them and have the differences shown, without writing the alignment command yourself.

04

Taking a measurement mid-discussion

Ask for the distance between two residues while you are talking about them.

05

Doing something nobody wrapped

Fall through to running Python inside PyMOL when the task is outside the usual commands.

06

Producing a figure

Set the view and save it as a high-resolution image from the same conversation.

BEFORE YOU INSTALL

What to know first

Requires

PyMOL installed on your system
Python 3.10 or newer
Git

Where it runs

The documented client runs the server on your machine.

INSTALLATION

Connect your client

This one is built from source rather than installed with a single command.

Server setup

TERMINAL

git clone https://github.com/vrtejus/pymol-mcp
cd pymol-mcp
python -m venv venv
source venv/bin/activate
pip install mcp

Open Claude Desktop, go to Claude > Settings > Developer > Edit Config, and add the configuration under MCP Clients to claude_desktop_config.json.

Install the PyMOL plugin: open PyMOL, go to Plugin → Plugin Manager → Install New Plugin, choose "Choose file..." and select pymol-mcp-socket-plugin/__init__.py in the cloned repository, then follow the prompts.

In PyMOL, go to Plugin → PyMOL MCP Socket Plugin and click "Start Listening". The status should change to "Listening on port 9876"; Claude can reach PyMOL only while it is listening, on the same machine.

MCP Clients

Claude Desktop

CLAUDE DESKTOP · JSON

{
  "mcpServers": {
    "pymol": {
      "command": "<YOUR_PATH_TO_VENV_PYTHON>",
      "args": [
        "<YOUR_PATH_TO_PYMOL_MCP_SERVER>"
      ]
    }
  }
}

Both bracketed values are full paths inside your clone, for example /Users/username/pymol-mcp/venv/bin/python and /Users/username/pymol-mcp/pymol_mcp_server.py. On Windows, use forward slashes.

PyMOL-MCP