ChimeraX MCP Server

Talk to proteins in natural language. This MCP server connects AI coding tools (Claude Code, Cursor, VS Code, etc.) to UCSF ChimeraX, letting you load, edit, visualize, and analyze protein structures through conversation -- no manual ChimeraX commands needed.

Just say "open 6VXX, mutate A:501 to Lys, color by hydrophobicity, and take a screenshot" and watch ChimeraX do it in real time.

This project is in early development and actively looking for contributors. Bug reports, feature requests, and pull requests are very welcome -- check out the issues page or open a PR!

Demos

Load & Visualize

"Load 3LJ5, show only chain A, make it publication-ready with rainbow coloring and transparent surface"

Mutate Residue

"Open 6VXX, zoom to residue A:501, highlight it, mutate Thr to Lys, show nearby residues"

Electrostatic & Hydrophobicity Surfaces

"Load 1AKI, show surface, color by electrostatic potential, then switch to hydrophobicity"

Features

• 39 tools covering structure loading, editing, visualization, measurement, selection, and video recording

• Auto-launches ChimeraX -- no manual setup needed, just install and go

• Works with any MCP client -- Claude Code, Cursor, Windsurf, VS Code Copilot, Cline, OpenCode, Continue, Claude Desktop

• Built-in agent instructions -- AI agents automatically learn ChimeraX spec syntax and common workflows

• Security hardened -- command injection prevention, dangerous command blocking, script path validation

• Accepts flexible input -- both A:48 and /A:48 spec formats, both 1-letter and 3-letter amino acid codes

• Video recording -- capture sessions as MP4, record turntable spins

• Run custom scripts -- execute .cxc and .py scripts with path validation

Prerequisites

• UCSF ChimeraX installed (download)

• Python 3.10+

ChimeraX will be launched automatically when the first tool is called. No need to start it manually or enable the REST API yourself.

Open ChimeraX and run in its command line:

remotecontrol rest start port 8765

To use a custom ChimeraX install location, set the CHIMERAX_BIN environment variable:

export CHIMERAX_BIN="/path/to/ChimeraX"

Installation

pip install chimerax-mcp

From GitHub (latest dev):

pip install git+https://github.com/mahynotch/chimerax-mcp.git

From source (development):

git clone https://github.com/mahynotch/chimerax-mcp.git
cd chimerax-mcp
pip install -e .

MCP Configuration

After installing, add the server to your AI coding tool:

claude mcp add -s user chimerax -- chimerax-mcp

Edit config file:

• macOS: ~/Library/Application Support/Claude/claude_desktop_config.json

• Windows: %APPDATA%\Claude\claude_desktop_config.json

• Linux: ~/.config/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project):

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": []
    }
  }
}

Add to .vscode/mcp.json:

{
  "servers": {
    "chimerax": {
      "type": "stdio",
      "command": "chimerax-mcp"
    }
  }
}

Use the "Edit MCP Settings" button in the Cline panel, or edit directly:

• macOS: ~/Library/Application Support/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json

• Windows: %APPDATA%\Code\User\globalStorage\saoudrizwan.claude-dev\settings\cline_mcp_settings.json

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp",
      "args": [],
      "disabled": false
    }
  }
}

Add to ~/.config/opencode/opencode.json or project opencode.json:

{
  "mcp": {
    "chimerax": {
      "type": "local",
      "command": ["chimerax-mcp"],
      "enabled": true
    }
  }
}

Add to .continue/config.yaml:

mcpServers:
  - name: chimerax
    type: stdio
    command: chimerax-mcp

Quick Start

Once configured, just talk naturally:

"Open 6VXX, color by chain, show surface, zoom to residue A:501"

The AI will call MCP tools sequentially and ChimeraX renders each step in real time:

1. open_structure("6VXX") -- fetches the structure from RCSB

2. color_structure("#1", "chain") -- colors each chain differently

3. show_surface("#1") -- displays the molecular surface

4. zoom_to("/A:501") -- centers the view on residue 501 of chain A

Available Tools (39)

Structure (6)

Editing (4)

Visualization (18)

Measurement (6)

Selection (5)

Security

Commands are sanitized before being sent to ChimeraX:

• Command injection blocked -- ; and newlines rejected (ChimeraX uses these as command separators)

• Dangerous commands blocked -- exec, shell, system are rejected

• Script execution validated -- run_script only accepts existing .cxc/.py files with path validation

• Local-only -- REST API listens on 127.0.0.1 only, not exposed to the network

Testing

Run the full test suite (53 tests) against a live ChimeraX instance:

pip install pytest
python -m pytest tests/test_live.py -v

Security tests run without ChimeraX. Live tests auto-skip if ChimeraX is not available.

For AI Agents: Auto-Install

If a user asks you to install this MCP server, follow these steps:

1. Install the package:

pip install chimerax-mcp

2. Register the MCP server (detect the user's tool and run the appropriate command):

For Cursor / VS Code / others, create or update the config file with:

{
  "mcpServers": {
    "chimerax": {
      "command": "chimerax-mcp"
    }
  }
}

3. Restart the AI tool to load the new MCP server.

4. Verify with a test call: open_structure("1aki")

Important: Before proceeding, confirm with the user that UCSF ChimeraX is installed on their machine. If not, direct them to https://www.cgl.ucsf.edu/chimerax/download.html -- the server auto-launches ChimeraX but cannot install it.

Disclaimer

This project is not affiliated with, endorsed by, or sponsored by UCSF or the RBVI team. "ChimeraX" is a trademark of the University of California. This server communicates with ChimeraX through its public REST API and contains no ChimeraX source code.

Users are responsible for complying with ChimeraX's license terms. ChimeraX is free for academic and non-commercial use; commercial use requires a separate license from UCSF.

License

MIT -- see LICENSE