molecular-visualization-3dmol

# 3Dmol.js molecular visualization ## Overview 3Dmol.js is a WebGL molecular viewer that runs entirely in the browser. This skill emits **self-contained HTML** files that load 3Dmol from a CDN and render a structure, a trajectory, or a vibrational mode — no server, no build step, no Python runtime to view. The bundled `scripts/mol_viewer.py` generates that HTML from any `.xyz/.trj/.pdb/.sdf/.mol2/.cube` file; the Core API below shows the underlying 3Dmol.js calls so you can hand-write or customize a viewer. ## When to Use - Animate a transition-state imaginary vibrational mode (from a mode trajectory or dx/dy/dz vectors) - Play back a reaction path (IRC/NEB) or an MD trajectory with a speed control - Show a protein–ligand docking pose with cartoon + ligand sticks + a binding-site surface - Display an orbital or electron-density isosurface from a Gaussian `.cube` file - Hand a colleague one HTML file that opens in any browser, no install - Use **py3Dmol** instead for inline viewers inside a Jupyter notebook (same engine, Python API) - Use **PyMOL/ChimeraX** instead for publication ray-traced stills or heavy structural editing - Use **rdkit-chemdraw-cdxml** for 2D chemical structures, **plotly/matplotlib** for 2D plots ## Prerequisites - **Viewing**: any modern browser with network access (the HTML pulls 3Dmol.js from a CDN) - **Generator script**: `scripts/mol_viewer.py` — Python 3 standard library only, no install - **Optional**: `pip install py3Dmol` for notebook use (...