iflow-mcp_pymol-mcp

# PyMOL-MCP: Integrating PyMOL with Claude AI 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. https://github.com/user-attachments/assets/687f43dc-d45e-477e-ac2b-7438e175cb36 ## Features - **Two-way communication**: Connect Claude AI to PyMOL through a socket-based server - **Intelligent command parsing**: Natural language processing for PyMOL commands - **Molecular visualization control**: Manipulate representations, colors, and views - **Structural analysis**: Perform measurements, alignments, and other analyses - **Code execution**: Run arbitrary Python code in PyMOL from Claude ## Installation Guide ### Prerequisites - PyMOL installed on your system - Claude for Desktop - Python 3.10 or newer - Git ### Step 1: Install the UV Package Manager **On macOS:** ```bash brew install uv ``` **On Windows:** ```bash powershell -c "irm https://astral.sh/uv/install.ps1 | iex" set Path=C:\Users\[YourUsername]\.local\bin;%Path% ``` For other platforms, visit the [UV installation guide](https://docs.astral.sh/uv/getting-started/installation/). ### Step 2: Clone the Repository ```bash git clone https://github.com/vrtejus/pymol-mcp cd pymol-mcp ``` ### Step 3: Set Up the Environment Create and activate a Python virtual environment: ```bash python -m venv venv ``` **On macOS/Linux:** ```bash source venv/bin/activate ``` **On Windows:** ```bash venv\Scripts\activate ``` ### Step 4: Install Dependencies With the virtual environment activated: ```bash pip install mcp ``` ### Step 5: Configure Claude Desktop 1. Open Claude Desktop 2. Go to Claude > Settings > Developer > Edit Config 3. This will open the `claude_desktop_config.json` file 4. Add the MCP server configuration: ```json { "mcpServers": { "pymol": { "command":…