pymol-setup

Print the following setup instructions to the user:

PyMOL MCP Plugin Setup

Step 1: Install PyMOL Socket Plugin

1. Open PyMOL
2. Go to Plugin > Plugin Manager > Install New Plugin
3. Click Choose file... and select:

   ~/.claude/plugins/pymol-skills/pymol-mcp-socket-plugin/__init__.py
   

4. Click OK to install

Step 2: Start the Socket Listener

Each time you want to use PyMOL with Claude:

1. Open PyMOL
2. Go to Plugin > PyMOL MCP Socket Plugin > Start Listening
3. You should see "Listening on port 9876" in the status

Step 3: Use PyMOL Commands

Now you can use natural language to control PyMOL:

• "Load protein 1UBQ and show as cartoon"
• "Color chain A red and chain B blue"
• "Align structure1 to structure2"

Troubleshooting

• Connection refused: Make sure PyMOL plugin is listening before using Claude
• Plugin not found: Reinstall the socket plugin in PyMOL