PyMolClaw

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

👥 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, 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:

align 1ubq with 4hhb and show me the RMSD
make a binding site figure of 1abc with ligand LIG
render 6m0j in Goodsell style
show the active site with catalytic residues in chain A
compare these two structures: 1ubq and 4hhb

Standalone Scripts

# Align two structures
python scripts/align.py --pdb1 1ubq --pdb2 4hhb --outdir /tmp/output

# Protein overview
python scripts/overview.py --pdb 1ubq --style cartoon --outdir /tmp/output

# Binding site
python scripts/binding_site.py --pdb 1abc --ligand LIG --outdir /tmp/output

# Goodsell style
python scripts/goodsell.py --pdb 6m0j --outdir /tmp/output

# Surface rendering
python scripts/surface.py --pdb 1ubq --style surface --outdir /tmp/output

# Active site
python scripts/active_site.py --pdb 1abc --residues "100,150,200" --chain A --outdir /tmp/output

# Spectrum coloring (B-factor/pLDDT)
python scripts/spectrum.py --pdb 1ubq --property bfactor --palette blue_white_red --outdir /tmp/output

Every script outputs three files:

• *.png — Rendered figure
• *.pse — PyMOL session (open in GUI to keep editing)
• *.pml — Reproducible PyMOL script

Prerequisites

PyMOL must be installed:

conda install -c conda-forge pymol-open-source

Verify:

pymol -c -q && echo "PyMOL ready"

Skill Installation (Claude Code)

# Clone directly
git clone https://github.com/junior1p/PyMolClaw.git ~/.claude/skills/pymol-claw

# Or ask an agent
# "Install the PyMolClaw skill from https://github.com/junior1p/PyMolClaw"

Architecture

PyMolClaw/
├── SKILL.md              # Main skill entry (trigger words + dispatch table)
├── README.md             # This file
├── references/
│   ├── recipes.md        # PyMOL scene recipes (from ChatMol)
│   └── commands.md       # PyMOL command cheat sheet
└── scripts/
    ├── align.py          # Structure alignment + RMSD
    ├── overview.py       # Protein overview
    ├── binding_site.py   # Ligand binding site
    ├── ppi.py            # Protein-protein interface
    ├── goodsell.py        # Goodsell-style illustration
    ├── surface.py        # Molecular surface
    ├── mutation.py       # Mutation site analysis
    ├── active_site.py    # Catalytic residues
    ├── distance.py       # Distances & contacts
    ├── spectrum.py       # Property coloring
    ├── density.py        # Density / EM maps
    ├── ensemble.py       # NMR / MD ensemble
    └── animation.py      # Tween animation

Example Output

Align 1ubq vs 4hhb

$ python scripts/align.py --pdb1 1ubq --pdb2 4hhb --outdir /tmp/output
RMSD: 5.760 Angstroms
Output: /tmp/output/aligned.png

Protein Overview

python scripts/overview.py --pdb 1ubq --style cartoon --outdir /tmp/output

License

MIT