pymol-mcp
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PyMOL-MCP enables seamless integration between PyMOL and Claude AI through the Model Context Protocol, facilitating conversationally directed molecular visualization and analysis. It features natural language command parsing and allows intelligent control of molecular structures from Claude AI.
PyMOL-MCP: Integrating PyMOL with Claude AI
PyMOL-MCP connects PyMOL to Claude AI via MCP, enabling conversational structural biology and molecular visualization.
Features
- 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
Installation Guide
- Install the UV Package Manager
- Clone the Repository
- Set Up the Environment
- Install Dependencies
- Configure Claude Desktop
- Install the PyMOL Plugin
Usage
- Start listening in PyMOL and access PyMOL tools in Claude Desktop using the hammer icon.
Troubleshooting
- Ensure PyMOL plugin is listening
- Check for command errors or installation issues
Limitations & Notes
- Socket connection requires both apps on the same machine
- Complex operations may require multiple steps
Contributing
Contributions are welcome! Submit a Pull Request.
License
This project is licensed under the MIT License.