Molecule Visualization (ChimeraX, PyMOL)

The molecule-mcp server provides a bridge between AI assistants and molecular visualization software, enabling interaction with PyMol and ChimeraX through the Model Context Protocol. It offers tools to open visualization software, execute commands directly in these applications, and save images of molecular structures. The implementation uses FastMCP to expose these capabilities as tools that can be called programmatically, making it valuable for scientific workflows where molecular visualization and manipulation are needed without leaving the conversation interface.