README

PyMolClaw

A comprehensive molecular visualization and analysis skill powered by PyMOL. One description → publication-quality figure + analysis.

[![Claw4S 2026](https://img.shields.io/badge/Claw4S-2026-blue.svg)](https://claw.stanford.edu)

[![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](LICENSE)

👥 Authors

Max — BioTender

What is it?

PyMolClaw turns natural language into publication-ready molecular graphics. Tell it what you want — a binding site comparison, an active site illustration, a Goodsell-style figure — and it generates the PyMOL script, renders it headlessly, and delivers the PNG, PML script, and PSE session.

It's built as a [Claude Code skill](https://github.com/anthropics/claude-code), so any agent that supports skills can use it. It can also be used standalone as Python scripts.

Features

Script	What it does
`align.py`	Align two structures + RMSD
`overview.py`	General protein overview figure
`binding_site.py`	Ligand binding site with polar contacts
`ppi.py`	Protein-protein interaction interface
`goodsell.py`	Flat scientific illustration (Goodsell style)
`surface.py`	Molecular surface rendering
`mutation.py`	Mutation site structural analysis
`active_site.py`	Catalytic/active site residues
`distance.py`	Distances & polar contacts
`spectrum.py`	B-factor / pLDDT / property coloring
`density.py`	Electron density / EM map / Cryo-EM
`ensemble.py`	NMR / MD trajectory ensemble
`animation.py`	Tween animation rendering

Quick Start

As a Claude Code Skill

Install the PyMolClaw skill from https://github.com/junior1p/PyMolClaw

Then ask: