Arcadia-Science/agentic-pymol

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# 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.

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