Molecule Visualization (ChimeraX, PyMOL)

🚀 Molecule-MCP

Molecule-MCP: A Model Context Protocol (MCP) server between molecular science-related tools and Claude AI. Molecule-MCP connects molecular science research tools with Claude AI, enabling Claude to directly manipulate these tools and serve as a partner to scientists. This integration enables prompt-assisted molecular modeling.

🚀 Quick Start

✨ Features

• Connect molecular science research tools with Claude AI.
• Enable Claude to directly manipulate tools and act as a scientific partner.
• Support prompt-assisted molecular modeling.

📦 Installation

⚠️ Important Note

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

1. Open Claude > Settings > Developer > Edit Configuration > claude_desktop_config.json, and add the following content:

{
  "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 scripts:

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

The path of mcp will be displayed. Copy this path and replace /path/to/mcp.

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

The path of molecule-mcp will be displayed. Copy this path and replace /path/to/molecule-mcp.

📄 License

Molecule-MCP is provided "as is" without warranty of any kind, either expressed 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. The user assumes all risks of using this software.

The authors are not responsible for any consequences arising from the use, misuse, or misunderstanding of this software or its output. Results obtained through Molecule-MCP should be independently verified in research, publications, or decision-making processes.

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