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Pymol MCP Server

PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This

Local serverstdioPython

What is the Pymol MCP Server?

PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful

What it actually does

  • Two-way communication — Connect Claude AI to PyMOL through a socket-based server
  • Intelligent command parsing — Natural language processing for PyMOL commands
  • Molecular visualization control — Manipulate representations, colors, and views
  • Structural analysis — Perform measurements, alignments, and other analyses
  • Code execution — Run arbitrary Python code in PyMOL from Claude

Configuration

  • PyMOL installed on your system - Claude for Desktop - Python 3.10 or newer - Git

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

How to install the Pymol MCP Server

{
  "mcpServers": {
    "pymol": {
      "command": "[Full path to your venv python]",
      "args": [
        "[Full path to pymol_mcp_server.py]"
      ]
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Configuration

  • PyMOL installed on your system - Claude for Desktop - Python 3.10 or newer - Git

Example prompts to try

  • “Use Pymol MCP to Prerequisites.”

Frequently asked questions

PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.

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