pymol

Render protein structures and measure distances with PyMOL headlessly.

2.7k|283|Updated May 13, 2026

Search Tags:#structure analysis #pymol #structural alignment #protein visualization #molecular rendering #binding site highlighting #protein-ligand interactions

Ready to run

npx skills add https://github.com/google-deepmind/science-skills --skill pymol-google-deepmind

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pymol
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/pymol
Command: npx skills add https://github.com/google-deepmind/science-skills --skill pymol-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires uv, pymol-open-source-whl, and includes references (resource) components.

What problem does it solve?

PyMOL eliminates the manual effort of creating publication-ready visualizations and measurements for protein and molecular structures.

Core Features & Use Cases

Headless structural rendering: Generate images (PNG) and save PyMOL session files (.pse) using software rendering (OSMesa) without needing a display or GPU.
Structural alignment and measurement: Perform superposition, alignments, and distance/contact analysis after verifying structures load correctly.
Visualization for structure biology and ligand inspection: Highlight binding sites or active residues, color by secondary structure or confidence/B-factor, and inspect protein-ligand interactions (without docking or molecular dynamics).

Quick Start

Ask the AI to render a protein cartoon colored by secondary structure from your local structure file and produce an output image plus a saved session file.

Frequently Asked Questions about pymol

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I render protein structures and save PyMOL session files without a display?▼

Headless rendering of protein structures uses OSMesa software rendering to generate PNG images and .pse session files without requiring a GPU or display.

Can I perform structural alignment and superposition using a local PDB file?▼

Yes, structural alignment and superposition are supported after verifying the local structure file loads correctly and atom counts are confirmed.

How do I highlight protein-ligand interactions and binding sites for publication images?▼

Visualizing protein-ligand interactions involves highlighting active residues and binding sites, applying secondary structure coloring to produce publication-ready images.

Does this PyMOL workflow support molecular dynamics or docking simulations?▼

No, this workflow focuses on structural visualization and static analysis; it does not perform molecular dynamics or docking simulations.

What is needed to automate structural analysis and distance measurements from a local structure file?▼

Automating distance measurements requires local structure files, host execution via uv, mandatory PyMOL initialization, and structure existence checks before analysis.

Why does headless molecular rendering require OSMesa and specific path handling?▼

Headless molecular rendering requires OSMesa for software rendering and project-root safe paths because standard display drivers are unavailable in headless environments.