ChimeraX MCP Server

A standalone Model Context Protocol (MCP) server that connects AI coding assistants to UCSF ChimeraX for molecular visualization and structural biology workflows.

About

ChimeraX MCP bridges the gap between conversational AI and molecular visualization. Instead of manually typing ChimeraX commands, you describe what you want in natural language — open structures, run analyses, generate publication figures — and the MCP server translates your intent into precise ChimeraX operations via its REST API.

The server handles everything automatically: discovering or launching ChimeraX instances, managing sessions across multiple ports, formatting results, and providing contextual error hints when something goes wrong.

Key capabilities:

• 119 specialized tools covering the full structural biology workflow
• Auto-launch — ChimeraX starts automatically when needed, no manual setup
• Multi-session — work with multiple ChimeraX instances simultaneously
• Input validation — atomspec validation and error hints for common mistakes
• Configurable — environment variables for ports, paths, timeouts, and debug logging

AI Assistant  -->  MCP (stdio)  -->  chimerax-mcp (Python)  -->  HTTP REST  -->  ChimeraX

Inspired by the RBVI official ChimeraX MCP bridge.

Prerequisites

• UCSF ChimeraX installed
• Python 3.11+
• A local MCP client such as Claude Code, Claude Desktop, Codex, Cursor, VS Code, Gemini CLI, or similar

Quick Install (Codex Desktop, Codex CLI, and more)

git clone https://github.com/dovas-net/chimeraX-mcp.git
cd chimeraX-mcp
./install.sh

That’s it. The script creates a Python venv in .venv/, installs the package, writes the MCP config for Codex (shared by Codex Desktop and the Codex CLI via ~/.codex/config.toml), and runs a doctor check.

After the script finishes, fully quit Codex Desktop (⌘Q — not just closing the window) and reopen it. The ChimeraX tools will appear on the next launch.

Install for a different client instead:

./install.sh claude-desktop
./install.sh cursor
./install.sh claude-code
./install.sh copilot
./install.sh gemini
./install.sh cline
./install.sh continue
./install.sh windsurf

Windows users: install.sh is bash-only. Follow the Manual Installation steps below in PowerShell.

Manual Installation

If you’d rather drive each step yourself or you’re developing the server:

git clone https://github.com/dovas-net/chimeraX-mcp.git
cd chimeraX-mcp
python3 -m venv .venv && source .venv/bin/activate
pip install .                    # or `pip install -e ".[dev]"` for development
chimerax-mcp setup codex         # or any other client name