Pymol

This skill lets Claude generate publication-quality molecular structure images using PyMOL in headless mode with OSMesa rendering. It's built for protein visualization tasks like secondary structure coloring, B-factor/pLDDT confidence mapping, binding site highlighting, and structural superposition. The skill includes ready-to-use recipes for common scenarios (AlphaFold confidence coloring, electrostatic surfaces, protein-ligand interactions) and enforces best practices like always saving PSE session files alongside PNGs so you can refine the view locally. It won't do docking or MD simulations, but for creating figures or quick structural analysis of PDB/CIF files you already have, it's solid. The uv-based setup with PEP 723 headers means zero manual dependency wrangling.

Install to Claude Code

npx -y skills add google-deepmind/science-skills --skill pymol --agent claude-code