PyMOL MCP Vis Server

Provides two-way PyMOL control and visual feedback via Claude AI for structural biology workflows.

python

0

GitHub Stars

python

Language

5 months ago

First Indexed

2 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "ryannmperez-pymol-mcp-vis": {
      "command": "/Users/username/pymol-mcp/venv/bin/python",
      "args": [
        "/Users/username/pymol-mcp/pymol_mcp_server.py"
      ],
      "env": {
        "MOCK_ENV": "value"
      }
    }
  }
}

You have a PyMOL MCP Server that lets Claude AI interact with PyMOL in real time, including visual feedback. This enables two-way communication, natural language to PyMOL command translation, and the ability to render and analyze molecular structures with live visual verification.

How to use

Launch the PyMOL MCP Server and connect Claude AI to it. In Claude, you will access PyMOL tools through the MCP connection and can issue commands in natural language. Claude will translate your requests into PyMOL actions, apply visual representations, run analyses, and reflect results on screen. You can ask Claude to load structures, color by properties, adjust representations, perform measurements, align structures, and save high‑quality images of the current view. The server supports a visual feedback loop: Claude can command PyMOL, wait for the result, and visually verify the outcome before proceeding.

Starting from a PyMOL session, ensure the MCP socket plugin is listening so Claude can connect. In Claude, click the PyMOL tool button (hammer icon) to begin an interactive session. From here you can ask Claude to load PDBs, display them as cartoons, highlight active sites, or compare structures by running measurements and alignments. Use natural language prompts like “Load PDB 1UBQ and display as cartoon” or “Highlight active site residues with sticks” and Claude will translate your request into PyMOL commands and then show the results visually.

Available tools

two_way_communication

Connect Claude AI to PyMOL through a socket-based server enabling two-way interaction.

nlp_command_parsing

Natural language processing for PyMOL commands to convert user prompts into actionable PyMOL steps.

visualization_control

Manipulate representations, colors, and views in PyMOL based on commands.

structural_analysis

Perform measurements, alignments, and other structural analyses inside PyMOL.

code_execution

Execute arbitrary Python code within PyMOL from Claude.