Command: mcp

Usage:
mcp setup

Usage:
mcp start [ port ]

Usage:
mcp info

Usage:
mcp stop

The mcp command enables ChimeraX to listen for commands from the Claude Desktop AI chatbot using the Model Context Protocol (MCP) developed by Anthropic. Running ChimeraX from Claude 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 setup – write a Claude Desktop configuration file to allow it to control ChimeraX using MCP; this only needs to be done once per computer and ChimeraX version. The configuration file name and location depend on the platform:
  • on Mac: ~/Library/Application Support/Claude/claude_desktop_config.json
  • on Windows: ~/AppData/Roaming/Claude/claude_desktop_config.json
• mcp start [ port ] – start the ChimeraX REST server for MCP bridge connections using port number port (default 8080); this is not required if ChimeraX is started by Claude
• mcp info – check to see if ChimeraX is listening for commands via REST server on localhost port 8080
• mcp stop – stop the ChimeraX REST server

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Set Up Claude Desktop to Control ChimeraX

1. Install Claude Desktop for Mac or Windows (not available for other platforms), 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 giving Claude a natural language request, e.g., “Show me a conotoxin protein in ChimeraX”