Molecule Visualization (ChimeraX, PyMOL)

Molecule-MCP: A model-context-protocol server for molecules. Molecule-MCP connects molecule science releated tools to Claude AI through the Model Context Protocol (MCP), allowing Claude to directly interact with and control these tools and act as a co-scientist. This integration enables prompt assisted molecule modeling.

Installation

⚠️ Note: Molecule-MCP requires Claude Desktop to be installed and running.

1. Go to Claude > Settings > Developer > Edit Config > claude_desktop_config.json to include the following:

{
  "mcpServers": {
    "pymol": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/pymol_server.py"
      ]
    },
    "chimerax": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/ChimeraX_server.py"
      ]
    },
    "gromacs_copilot": {
      "command": "/path/to/mcp",
      "args": [
        "run",
        "/path/to/molecule-mcp/mcp_server.py"
      ]
    }
  }
}

2. Install mcp and get the script

pip install "mcp[cli]" chatmol
pip install git+https://github.com/ChatMol/gromacs_copilot.git # optional, for running gromacs_copilot
which mcp

the path to mcp will be displayed. Copy this path for the next step and replace /path/to/mcp with the path to mcp.

git clone https://github.com/ChatMol/molecule-mcp.git
cd molecule-mcp
pwd

the path to molecule-mcp will be displayed. Copy this path for the next step and replace /path/to/molecule-mcp with the path to molecule-mcp.

Disclaimer

Molecule-MCP is provided "as is" without warranty of any kind, express or implied. The authors and contributors disclaim all warranties including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Users employ this software at their own risk.

The authors bear no responsibility for any consequences arising from the use, misuse, or misinterpretation of this software or its outputs. Results obtained through Molecule-MCP should be independently validated prior to use in research, publications, or decision-making processes.

This software is intended for research and educational purposes only. Users are solely responsible for ensuring compliance with applicable laws, regulations, and ethical standards in their jurisdiction.