chimerax-mcp
Overview
chimerax-mcp is a Python Model Context Protocol (MCP) server that connects AI coding tools to UCSF ChimeraX for natural-language protein editing and molecular structure manipulation.
Capabilities
- • stdio transport support
- • github integration
- • mcp client integration
- • workflow automation support
Best For
MCP server enabling AI tools to interact with UCSF ChimeraX for natural language protein editing, molecular visualization and structural biology work.
Decision Snapshot
Install
available
Usage
available
Config
7 strong hints
Capabilities
4 key capabilities detected
- • Source provenance count: 1
- • Last seen: 4/3/2026
- • Published: 4/3/2026
Installation / Setup
pip install chimerax-mcp
Usage
claude mcp add -s user chimerax -- chimerax-mcp
Features
- • **39 tools** covering structure loading, editing, visualization, measurement, selection, and video recording
- • **Auto-launches ChimeraX** -- no manual setup needed, just install and go
- • **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
- • stdio transport support
Use Cases
- • Supports capabilities such as: stdio transport support; github integration; mcp client integration.
- • Common usage themes: chimerax, mcp, model-context-protocol, molecular-visualization.
Supported Clients / Integrations
- • stdio transport support
- • github integration
- • mcp client integration
- • workflow automation support
Compatibility Signals
- • GitHub: supports (Detected in parser config/capability hints.)
Prompt Examples
example
• claude mcp add -s user chimerax -- chimerax-mcp
Notes / Requirements
- • Primary language: Python
- • License: MIT
- • Parser coverage score: 1.00
- • Source feeds: PyPI RSS + JSON API
- • Topic cluster: general
Official Links
Source Information
You can verify all information on this page against the source repository above.
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