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

powershell -c "irm https://astral.sh/uv/install.ps1 | iex" set Path=C:\Users\[YourUsername]\.local\bin;%Path%

For other platforms, visit theUV installation guide.

git clone https://github.com/vrtejus/pymol-mcp cd pymol-mcp

{ "mcpServers": { "pymol": { "command": "[Full path to your venv python]", "args": ["[Full path to pymol_mcp_server.py]"] } } }

{ "mcpServers": { "pymol": { "command": "/Users/username/pymol-mcp/venv/bin/python", "args": ["/Users/username/pymol-mcp/pymol_mcp_server.py"] } } }

Note:Use the actual full paths on your system. On Windows, use forward slashes (/) instead of backslashes.
- Open PyMOL
- Go to Plugin → Plugin Manager
- Click on "Install New Plugin" tab
- Select "Choose file..." and navigate to the cloned repository
- Select thepymol-mcp-socket-plugin/__init__.pyfile
- Click "Open" and follow the prompts to install the plugin

- Go to Plugin → PyMOL MCP Socket Plugin
- Click "Start Listening"
- The status should change to "Listening on port 9876"

- You should see a hammer icon in the tools section when chatting
- Click it to access the PyMOL tools

Here are some examples of what you can ask Claude to do:

- "Load PDB 1UBQ and display it as cartoon"
- "Color the protein by secondary structure"
- "Highlight the active site residues with sticks representation"
- "Align two structures and show their differences"
- "Calculate the distance between these two residues"
- "Save this view as a high-resolution image"

- Connection issues: Make sure the PyMOL plugin is listening before attempting to connect from Claude
- Command errors: Check the PyMOL output window for any error messages
- Plugin not appearing: Restart PyMOL and check that the plugin was correctly installed
- Claude not connecting: Verify the paths in your Claude configuration file are correct

- The socket connection requires both PyMOL and Claude to be running on the same machine
- Some complex operations may need to be broken down into simpler steps
- Always save your work before using experimental features
- Join our Bio-MCP Community to troubleshoot, provide feedback & improve Bio-MCPS