pymol-mcp
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.
What are the prerequisites for using PyMOL-MCP?
You need to have PyMOL installed, Claude for Desktop, Python 3.10 or newer, and Git.
How do I start the connection between PyMOL and Claude?
In PyMOL, start the PyMOL MCP Socket Plugin and click 'Start Listening'. In Claude Desktop, access the PyMOL tools via the hammer icon in the tools section.
What should I do if the plugin does not appear in PyMOL?
Restart PyMOL and ensure that the plugin was correctly installed.
Can I use PyMOL-MCP on different machines?
No, the socket connection requires both PyMOL and Claude to be running on the same machine.
What are some example commands I can use with Claude?
You can ask Claude to load PDB files, color proteins, highlight residues, align structures, calculate distances, and save views as images.