PyMOL-Claude

MOLAI v0.1.0

PyMOL-Claude Integration

A direct integration between Claude AI and PyMOL molecular visualization software, enabling Claude to control and manipulate molecular structures in PyMOL.

Overview

This project provides a seamless integration between Anthropic's Claude AI assistant and the PyMOL molecular visualization program. With this integration, you can:

Send PyMOL commands directly from Claude
Visualize and manipulate molecular structures
Create complex molecular representations
Automate PyMOL workflows through natural language

Components

The integration consists of three main components:

MCP Server Script - A script that handles Model Context Protocol (MCP) communication between Claude and PyMOL
PyMOL Plugin - A plugin for PyMOL that enables direct communication with Claude
Claude Desktop Configuration - Configuration for Claude Desktop to connect to the MCP server

Quick Start

For a quick deployment, use the files in the FINAL directory:

Copy the pymol_mcp.py script to a location accessible to Claude Desktop
Copy the claude_plugin directory to your PyMOL plugins directory, or go to Plugin -> Plugin Manager to load the init.py and pymol_claude.py files
Update your Claude Desktop configuration to point to the MCP script, and update the filesystem paths as appropriate.
Start PyMOL and then start Claude Desktop

See the FINAL/README.md for detailed deployment instructions.

Examples

After setting up the integration, you can send commands to PyMOL directly from Claude:

fetch 1LG5
show cartoon
color spectrum
zoom

Development

If you want to modify or extend the integration, see the development guide in docs/DEVELOPMENT.md.

License

This project is licensed under a hybrid MIT - Ligandal License - see the LICENSE file for details.

Acknowledgments

Anthropic for developing Claude AI
PyMOL developers for the powerful molecular visualization software
This integration was created by Andre Watson (@nanogenomic)