PyMOL

The PyMOL MCP server provides a bridge between Claude and the PyMOL molecular visualization software, enabling interactive protein structure analysis through a comprehensive set of tools. Built with Python using the FastMCP framework, it offers capabilities for loading structures from PDB files, manipulating visualizations with different representations and colors, measuring molecular distances and angles, and rendering high-quality images. The implementation includes robust error handling and logging, making it particularly valuable for researchers and educators who need to analyze protein structures, examine binding sites, or create publication-quality molecular visualizations through natural language instructions.