Command: mcp

Usage:
mcp start [ port ]

Usage:
mcp stop

Usage:
mcp info

Usage:
mcp setup

The mcp command enables ChimeraX to listen for commands from the Claude AI chatbot using the Model Context Protocol developed by Anthropic. The capability for Claude to interact with ChimeraX was first implemented by Alexis Rohou at Genentech and subsequently incorporated into ChimeraX as the mcp command. See also: remotecontrol, Claude Chat to Operate ChimeraX

• mcp start [ port ] – start the ChimeraX REST server for MCP bridge connections using port number port (default 8080)
• mcp stop – stop the ChimeraX REST server
• mcp info – check to see if ChimeraX is listening for commands via REST server on localhost port 8080
• mcp setup – write Claude Desktop configuration file to allow it to control ChimeraX using MCP. The file name and location depends on the platform:
  • on Mac: ~/Library/Application Support/Claude/claude_desktop_config.json
  • on Windows: ~/AppData/Roaming/Claude/claude_desktop_config.json

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Set Up Claude Desktop to Control ChimeraX

1. Install Claude Desktop on Mac or Windows, start it, and create a free account.
2. Start ChimeraX and enter command mcp setup to generate the configuration file needed for Claude Desktop to control ChimeraX.
3. Quit Claude Desktop and ChimeraX. Make sure to use Claude menu File / Exit when quitting; due to a bug in Claude Desktop (version 1.0.1405), closing it with the window frame "X" button leaves hidden Claude subprocesses running that will prevent it from reading the configuration file when restarted.
4. Restart Claude Desktop and test by typing into Claude “Show me a conotoxin protein in ChimeraX”.