{"repo":"Arcadia-Science/agentic-pymol","free":true,"listed":false,"github":"https://github.com/Arcadia-Science/agentic-pymol","clone":"git clone https://github.com/Arcadia-Science/agentic-pymol.git","description":"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)","language":"Python","stars":89,"topics":[],"license":"MIT","category":"mcp-servers","readme_excerpt":"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: For a brief showcase of abilities, see this 6-minute demonstration of how you can use Agentic PyMOL to conduct meaningful structural analysis with natural language: Design goals - Use the PyMOL you already have. Works with your existing PyMOL installation; PyMOL 2.6+ is supported. - No insular chatbot. PyMOL is exposed to your general-purpose agent rather than wrapping PyMOL in its own chat interface. - Two-way communication. The agent can manipulate the live PyMOL session and read structured information back out for reasoning, answers, and downstream work. - Typed over textual. Return objects, chains, coordinates, distances, RMSDs, views, sequences, and errors as data -- not just “succeeded.” - PyMOL-native first. Stay focused on visualization, selection logic, geometry, alignments, rendering, and session inspection. - Lightweight and composa","default_branch":null,"files":null,"tree":[],"storefront":"/r/Arcadia-Science","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Arcadia-Science/agentic-pymol/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}