PyMOL-MCP
by vrtejus
PyMOL-MCP connects PyMOL to Claude AI through the Model Context Protocol (MCP), enabling Claude to directly interact with and control PyMOL. This powerful integration allows for conversational structural biology, molecular visualization, and analysis through natural language.
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What is PyMOL-MCP?
PyMOL-MCP is a tool that integrates PyMOL with Claude AI using the Model Context Protocol (MCP). This allows Claude AI to control PyMOL through natural language commands, enabling conversational structural biology.
How to use PyMOL-MCP?
To use PyMOL-MCP, you need to install PyMOL and Claude Desktop, clone the repository, set up a Python virtual environment, install dependencies, configure Claude Desktop with the MCP server details, and install the PyMOL plugin. Once configured, start the connection in PyMOL and Claude Desktop, and then use natural language commands in Claude to control PyMOL.
Key features of PyMOL-MCP
Two-way communication between Claude AI and PyMOL
Intelligent command parsing using natural language processing
Molecular visualization control (representations, colors, views)
Structural analysis (measurements, alignments)
Code execution: Run arbitrary Python code in PyMOL from Claude
Use cases of PyMOL-MCP
Conversational structural biology
Molecular visualization through natural language
Automated structural analysis
Interactive tutorials for PyMOL
Remote control of PyMOL
FAQ from PyMOL-MCP
What if I have connection issues?
What if I have connection issues?
Make sure the PyMOL plugin is listening before attempting to connect from Claude.
What if I encounter command errors?
What if I encounter command errors?
Check the PyMOL output window for any error messages.
What if the plugin is not appearing?
What if the plugin is not appearing?
Restart PyMOL and check that the plugin was correctly installed.
What if Claude is not connecting?
What if Claude is not connecting?
Verify the paths in your Claude configuration file are correct.
Can I use PyMOL-MCP on different machines?
Can I use PyMOL-MCP on different machines?
The socket connection requires both PyMOL and Claude to be running on the same machine.