py3Dmol

Use when creating 3D molecular visualizations with py3Dmol (3Dmol.js). Covers PDB/SDF/SMILES loading, cartoon/stick/sphere styles, protein-ligand complexes, docking pose viewers, selection language, PNG/HTML export, and NGLview for MD trajectories.

py3Dmol — Molecular Visualization

Purpose

Interactive 3D molecular visualization in Jupyter notebooks and scripts. Wraps 3Dmol.js (WebGL). Used for docking pose inspection, protein-ligand complexes, conformer overlays, trajectory snapshots.

When to Use This Skill

  • Visualizing docking poses from Vina/Gnina
  • Inspecting protein-ligand binding pockets
  • Displaying conformer ensembles
  • Annotating pharmacophore features on 3D structures
  • Quick structure QC after homology modeling or MD prep

Reference Files

FileContent
references/basics.mdInstallation, view creation, loading PDB/SDF/SMILES, stick/sphere/cartoon/surface basics
references/protein-ligand.mdProtein+ligand display, binding pocket zoom, dual-structure overlay, docking pose batch
references/selections-styles.mdSelection language (chain/resi/resn/atom), color schemes, surfaces, labels, transparency
references/jupyter-patterns.mdJupyter embed, ipywidgets sliders, NGLview alternative, saving PNG, RDKit interop

Quick Routing

"Show me a docking pose" → protein-ligand.md

"Show all conformers overlaid" → jupyter-patterns.md (animation loop)

"Highlight binding pocket / surface" → selections-styles.md

"I just need a quick look at a molecule" → basics.md

Minimal Pattern

import py3Dmol

view = py3Dmol.view(width=800, height=500)
view.addModel(open('complex.pdb').read(), 'pdb')
view.setStyle({'cartoon': {'color': 'spectrum'}})   # protein
view.setStyle({'resn': 'LIG'}, {'stick': {'colorscheme': 'greenCarbon'}})
view.zoomTo({'resn': 'LIG'})
view.show()

Key Facts

  • py3Dmol renders via 3Dmol.js in Jupyter — requires a running notebook kernel
  • For non-Jupyter contexts: use view.png() → base64 PNG, or view.write_html()
  • NGLview is an alternative with better trajectory support (use for MD)
  • setStyle is cumulative by default; use setStyle({}, {}) to reset all
  • Ligand residue name varies: 'LIG', 'UNL', 'MOL' — check with grep before scripting