Command: mcp

Usage:
mcp setup [ host claude | cursor | vscode | all ]

Usage:
mcp start [ port ]

Usage:
mcp info

Usage:
mcp stop

The mcp command enables ChimeraX to be controlled by an MCP-capable AI assistant — for example Claude Desktop, Cursor, or VS Code with GitHub Copilot — using the Model Context Protocol (MCP) developed by Anthropic. Running ChimeraX from an AI assistant 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 [ host host-name ] – write a configuration file telling an MCP-capable AI assistant how to launch the ChimeraX MCP bridge. The optional host keyword selects which assistant to configure; this only needs to be done once per host per ChimeraX version. Supported hosts and the resulting config files are:
  • claude (default) – Claude Desktop:
    • on Mac: ~/Library/Application Support/Claude/claude_desktop_config.json
    • on Windows: ~/AppData/Roaming/Claude/claude_desktop_config.json
  • cursor – Cursor (global config, applied to every project):
    • on all platforms: ~/.cursor/mcp.json (Cursor's documentation specifies this same path on Mac, Linux, and Windows)
  • vscode – VS Code with GitHub Copilot MCP servers (user-profile config, applied to every workspace):
    • on Mac: ~/Library/Application Support/Code/User/mcp.json
    • on Linux: ~/.config/Code/User/mcp.json
    • on Windows: ~/AppData/Roaming/Code/User/mcp.json
  • all – configure every supported host whose config directory is present on this machine.
• mcp start [ port ] – start the ChimeraX REST server for MCP bridge connections using port number port (default 8080); this is not required if the AI assistant launches ChimeraX itself.
• mcp info – for each supported host, report whether it is configured to use this ChimeraX. Also report whether the ChimeraX REST server is currently running and, if so, on which port and whether JSON output and logging (both required by the MCP bridge) are enabled.
• mcp stop – stop the ChimeraX REST server

[back to top: mcp]

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”

Set Up Cursor to Control ChimeraX

1. Install Cursor and run it at least once so that the ~/.cursor directory is created (this is the same path on Mac, Linux, and Windows).
2. In ChimeraX, run mcp setup host cursor. This writes ChimeraX's bridge entry into Cursor's global mcp.json.
3. Restart Cursor (or use Cursor's "Reload MCP servers" action) and ask the chat to perform a ChimeraX action.

Set Up VS Code Copilot to Control ChimeraX

1. Install VS Code with GitHub Copilot and ensure MCP support is enabled.
2. In ChimeraX, run mcp setup host vscode. This writes ChimeraX's bridge entry into the user-profile mcp.json in the form expected by VS Code (top-level servers key, with "type": "stdio").
3. In VS Code, run the command palette action MCP: List Servers to verify that the chimerax server is listed, then start it from there or simply ask Copilot to perform a ChimeraX action.