agentic-pymol MCP Server
Arcadia-Science/agentic-pymol
[](https://agentrank-ai.com/tool/Arcadia-Science--agentic-pymol/?utm_source=badge&utm_medium=readme&utm_campaign=agentrank_badge) A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)
claude mcp add agentrank -- npx -y agentrank-mcp-server Overview
Arcadia-Science/agentic-pymol is a Python MCP server licensed under MIT. A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)
Ranked #6678 out of 24846 indexed tools.
Ecosystem
Score Breakdown
105 stars → growing community
Last commit 1mo ago → moderate activity
0/2 issues closed → many open issues
5 contributors → small team
No dependents → no downstream usage
Weights: Freshness 20% · Issue Health 20% · Dependents 22% · Stars 10% · Contributors 8% · How we score →
How to Improve
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From the README
# Agentic PyMOL https://github.com/user-attachments/assets/43524828-0fcc-44e5-bcd6-c912e7f865b1 ## Description A lightweight Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface for general-purpose agents. Use it with Claude Code, Claude Desktop, Codex, or any MCP-compatible client to let your agent control an open PyMOL session, inspect molecular structures, run PyMOL-native analyses, and render what it sees. Agentic PyMOL is not an embedded chatbot and not a molecular workbench. It is a small bridge between a capable agent and the PyMOL session you already use. ## What you can do Ask your agent to use PyMOL directly: ```text * Fetch ubiquitin, show it as cartoon, color by secondary structure, and render a PNG. * Create a table of residues that are in contact with DNA in the DNA-binding protein 6EDC. * Load these two structures, align chain A, report the RMSD, and show the regions that moved the most. * Which of these 10 binders trigger a conformationRead full README on GitHub →
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