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.

skills.sh installs: 2.3K
GitHub stars: 3.4K
last updated: Aug 21, 2026

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Install

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

Installs into .claude/skills of the current project.

Files

PyMOL

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If .licenses/pymol_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the license at https://www.pymol.org/, then (2) create the file recording the notification text and timestamp.

Overview

All PyMOL commands run on the host via uv with OSMesa software rendering — no GPU, display, or X server is needed. Structure files must be downloaded to the host before running PyMOL.

Do NOT use when:

The user wants to run AlphaFold predictions.
The user wants docking or molecular dynamics simulations.
The user only has a sequence and no structure file — fetch the structure first. Check if any other installed skills can retrieve structures from the PDB or AlphaFold Database before proceeding.