MCP server that connects Claude Code to a live PyMOL session over XML-RPC
An MCP server that lets Claude Code drive a live PyMOL session — fetch structures, build selections, adjust representations and coloring, measure distances — by talking to PyMOL's built-in XML-RPC server.
PyMOL ships with an XML-RPC server (enabled via pymol -R) that exposes its command API on localhost:9123. pymolserver.py wraps that in three MCP tools so Claude can call them like any other tool:
Tool Purpose ------ pymolcommand Run one PyMOL command, exactly as you'd type it at the PyMOL prompt pymolscript Run a block of Python inside PyMOL's embedded interpreter (loops, cmd. calls, etc.) pymolquery Call any PyMOL XML-RPC method directly and get the return value back (for read-only lookups like atom counts or chain lists)
Claude decides which tool fits the request and supplies the PyMOL command or code itself — this server is just the transport layer.
- PyMOL (with XML-RPC support — the open-source build includes it) - Claude Code: npm install -g @anthropic-ai/claude-code - Python 3.10+
1. Clone this repo and install dependencies
2. Make PyMOL start its RPC server automatically (optional but recommended)
By default you'd need to launch PyMOL from a terminal with pymol -R every time. Instead, symlink autostart/pymolrc.py to ~/.pymolrc.py — a script PyMOL runs on every launch — so RPC starts silently whether you open PyMOL from the command line, Spotlight, or the Dock:
From now on, just open PyMOL normally. It listens for the MCP server on port 9123 (override with PYMOLRPCPORT).
From the project README.
Add the radar badge to your README — it shows your project was picked up by MCP Radar and links to this page:
[](https://mcp.liqiwa.com/s/stavasol96-arch--Pymol-Claude-MCP.html)
Stop your AI from making things up — it proposes, deterministic tools decide, every claim checked against ground truth with evidence. Grounded facts and context survive resets. Reverse engineering is
zhuyansen/new-term-radarDaily radar for new AI terms: names of new models, products and repos, caught on X, Hugging Face, GitHub and sitemaps before keyword tools list them.
yzg1226/mcd-party-officer🍟 麦当劳门店派对成团调度 Skill — 把派对从「策划」推进到「办得成」：成团概率雷达 / 包场vs拼团 / 择日黄历 / 儿童营养指数 / 招募卡与邀请函
fellowgeek/mcp-memoryAn OKF-backed Model Context Protocol (MCP) server delivering persistent long-term memory and SQLite FTS5 search for AI agents.
hirotomasato/yowesGenerate realistic teacher documents (ID cards, licenses, letters) for 13 countries via MCP.
hujjun/mcd-saver-strategist麦当劳省钱点餐助手（麦门精算师）｜麦当劳优惠券组合优化 Skill：拉取麦当劳菜单与全部可用优惠券，算出最省的点餐组合，巨无霸套餐 ¥47 → ¥21.9（省 53%）。McDonalds MCP（麦当劳 MCP）coupon optimizer · McDonalds China MCP Server · Agent Skill for WorkBuddy · 麦当劳程序员创意开发大赛参赛作品
The top new MCP servers of the week, every Monday. No spam, unsubscribe anytime.