molecular-visualization-3dmol

name	molecular-visualization-3dmol
description	3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.
license	BSD-3-Clause

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 (wraps the same library)

No package is needed to produce or open the HTML. The generator lives in this skill's scripts/ folder (next to this SKILL.md). It can't be run in place from the skill directory, so use your file tools to read scripts/mol_viewer.py and save it into your working directory before running.

Quick Start

# animate a mode/trajectory file with play/pause + speed slider, in one call
python3 mol_viewer.py ts_imaginary_mode_000.trj --mode trajectory \
    --title "TS mode" --subtitle "-621.8 cm-1" --out ts_mode.html
# static structure:  python3 mol_viewer.py mol.xyz --out mol.html

Core API

All snippets assume <script src="https://3Dmol.org/build/3Dmol-min.js"></script> is loaded and a <div id="v"></div> exists.

Create a viewer and load a structure

createViewer binds to a div; addModel(data, format) loads coordinates. Always zoomTo() then render(). Supported format: xyz, pdb, sdf, mol2, cube, cif.

const viewer = $3Dmol.createViewer("v", {backgroundColor: "white"});
viewer.addModel(xyzString, "xyz");         // coordinates as a string, not a URL
viewer.setStyle({}, {stick: {radius: 0.15}, sphere: {scale: 0.28}});
viewer.zoomTo();
viewer.render();

Styles and coloring

setStyle(selection, styleSpec) — empty selection {} targets all atoms. Styles: stick, sphere, line, cross, cartoon. Color by element (default), a scheme, or a fixed color.

viewer.setStyle({}, {stick: {}, sphere: {scale: 0.25}});          // ball-and-stick
viewer.setStyle({elem: "C"}, {stick: {color: "gray"}});           // per-element override
viewer.setStyle({chain: "A"}, {cartoon: {color: "spectrum"}});    // protein ribbon
viewer.render();

Animate a trajectory

Load every frame with addModelsAsFrames, then animate. interval is the delay between frames in milliseconds (larger = slower) — do not use step, which skips frames and looks jumpy. loop: "backAndForth" makes a one-way path oscillate; reps: 0 loops forever.

viewer.addModelsAsFrames(trjString, "xyz");   // multi-frame .trj or multi-model .xyz/.pdb
viewer.setStyle({}, {stick: {radius: 0.14}, sphere: {scale: 0.28}});
viewer.zoomTo();
viewer.render();
viewer.animate({loop: "backAndForth", interval: 120, reps: 0});

Animate a vibrational normal mode

If a model's atoms carry displacement vectors (dx, dy, dz — extra columns on each XYZ line: elem x y z dx dy dz), model.vibrate(numFrames, amplitude, bothWays, arrowSpec) builds the oscillation frames. bothWays: true swings symmetrically about equilibrium; arrowSpec draws motion arrows.

const m = viewer.addModel(modeXyz, "xyz");        // each atom line: elem x y z dx dy dz
m.vibrate(10, 1.0, true, {radius: 0.08, color: "black"});   // 10 frames, full amplitude, arrows
viewer.setStyle({}, {stick: {radius: 0.14}, sphere: {scale: 0.28}});
viewer.zoomTo();
viewer.render();
viewer.animate({loop: "backAndForth", interval: 120, reps: 0});

If you only have a precomputed frame trajectory (e.g. pysisyphus ts_imaginary_mode_000.trj), use the trajectory path above instead — no dx/dy/dz needed.

Surfaces and volumetric isosurfaces

addSurface(type, style, atomsel) builds a molecular surface (VDW, SAS, SES, MS). For an orbital/density isosurface, load the .cube and call addVolumetricData.

viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity: 0.75, color: "lightblue"}, {chain: "A"});
// isosurface from a Gaussian cube (positive and negative lobes):
viewer.addVolumetricData(cubeString, "cube", {isoval:  0.02, color: "blue", opacity: 0.85});
viewer.addVolumetricData(cubeString, "cube", {isoval: -0.02, color: "red",  opacity: 0.85});
viewer.render();

Labels and interactive speed control

addLabel(text, spec) annotates. For animations, a slider bound to interval (restarting via stopAnimate() + animate()) lets the viewer set the speed — the fix for "sometimes too fast".

viewer.addLabel("TS", {position: {x: 0, y: 0, z: 0}, backgroundColor: "black", fontSize: 14});
let interval = 140;
const play = () => viewer.animate({loop: "backAndForth", interval});
document.getElementById("spd").oninput = e => { interval = +e.target.value; viewer.stopAnimate(); play(); };
play();

Key Concepts

interval vs step. interval (ms) sets playback speed; every frame is shown. step plays every Nth frame — it skips motion and is the usual cause of a "too fast"/jumpy animation. Control speed with interval, never step.

Coordinates are strings, not URLs. addModel/addModelsAsFrames take the file contents. Embed them in the HTML as a JSON-encoded string so quotes and newlines survive (scripts/mol_viewer.py uses json.dumps; a raw backtick template breaks on backticks in data).

CDN and CSP. The page fetches 3Dmol.js from a CDN, so it needs network access when opened, and a strict Content-Security-Policy (e.g. inside some artifact sandboxes) will blank it. Open it as a normal local/hosted file.

Common Workflows

TS imaginary-mode animation (quantum-chemistry)

End-to-end HTML from a precomputed mode trajectory, with play/pause and a speed slider — the deliverable the neb-irc-activation-energy skill hands off.

python3 mol_viewer.py ts_imaginary_mode_000.trj --mode trajectory \
    --title "Transition-state mode" --subtitle "-621.8 cm-1" --out ts_mode.html
# open ts_mode.html; drag the slider if the oscillation is too fast

Reaction-path / MD playback

python3 mol_viewer.py trajectory.pdb --mode trajectory --style ballstick --out md.html
# any multi-model .xyz/.pdb works; backAndForth loop + interval control are built in

Docking pose: protein ribbon + ligand sticks + pocket surface

const viewer = $3Dmol.createViewer("v", {backgroundColor: "white"});
viewer.addModel(complexPdb, "pdb");
viewer.setStyle({}, {cartoon: {color: "spectrum"}});                 // protein
viewer.setStyle({resn: "LIG"}, {stick: {radius: 0.2}});             // ligand
viewer.addSurface($3Dmol.SurfaceType.VDW, {opacity: 0.6}, {resn: "LIG", byres: true, expand: 5});
viewer.zoomTo({resn: "LIG"});
viewer.render();

Key Parameters

Parameter	Method	Default	Range / Options	Effect
interval	animate	50	40–400 ms	Frame delay; larger = slower playback
loop	animate	forward	forward/backward/backAndForth	backAndForth oscillates a one-way path
reps	animate	0	0=∞, n	Number of loops
radius	stick	0.3	0.1–0.3	Bond cylinder thickness
scale	sphere	1.0 (vdW)	0.2–0.4 for ball-and-stick	Atom sphere size
amplitude	vibrate	1.0	0.5–2.0	Normal-mode distortion size
numFrames	vibrate	10	8–20	Frames per half-cycle
isoval	addVolumetricData	—	e.g. ±0.02	Isosurface contour value (sign = lobe)
opacity	addSurface	1.0	0–1	Surface transparency

Best Practices

• Control animation speed with interval (ms), never step.
• Embed coordinates as a JSON-encoded string (json.dumps), not a raw backtick template.
• Call zoomTo() before render(), and again after adding a large model.
• Keep default element colors unless the analysis needs a specific scheme — don't bake a palette.
• For large trajectories (>500 frames or >5k atoms), subsample frames; WebGL redraw is the limit.
• Ship one CDN <script> tag; only vendor the ~1 MB 3Dmol-min.js inline if offline use is required.

Common Recipes

Recipe: generate a viewer in one call

python3 mol_viewer.py mode.xyz --mode vibrate --amplitude 1.2 --title "mode" --out mode.html
python3 mol_viewer.py mol.sdf  --style stick --out mol.html          # static

Recipe: inline viewer in a Jupyter notebook (py3Dmol)

import py3Dmol
view = py3Dmol.view(width=500, height=400)
view.addModel(open("mol.xyz").read(), "xyz")
view.setStyle({}, {"stick": {}, "sphere": {"scale": 0.25}})
view.zoomTo(); view.show()

Recipe: side-by-side viewers

const viewer = $3Dmol.createViewerGrid("v", {rows: 1, cols: 2});
viewer[0][0].addModel(reactantXyz, "xyz"); viewer[0][0].setStyle({}, {stick: {}});
viewer[0][1].addModel(productXyz, "xyz");  viewer[0][1].setStyle({}, {stick: {}});
viewer[0][0].zoomTo(); viewer[0][1].zoomTo(); viewer[0][0].render(); viewer[0][1].render();

Troubleshooting

Problem	Cause	Solution
Blank white page	3Dmol.js not loaded (offline / strict CSP)	Open with network access; check the CDN <script> resolves
Animation too fast / jumpy	Using step, or a tiny interval	Use interval (ms); raise it; never set step
Vibration shows no motion	Model lacks dx/dy/dz vectors	Add mode vectors as extra XYZ columns, or use a precomputed frame .trj
Nothing rendered	Wrong format string or bad data	Match format to the file; coordinates must be the file contents, not a path
JS syntax error in page	Backtick/quote in embedded data	Embed via json.dumps (the generator does this)
Structure loads but no bonds	XYZ without connectivity + line style	Use stick/sphere; 3Dmol infers bonds by distance
Surface slow or hangs	Large SES/MS on a big system	Use VDW, restrict the atomsel, or lower resolution

Bundled Resources

• scripts/mol_viewer.py — emit a standalone 3Dmol HTML (static / trajectory / vibrate) from a structure file, with built-in play/pause + speed slider for animations

Related Skills

• neb-irc-activation-energy — produces TS imaginary-mode trajectories and IRC paths that this skill animates
• rdkit-chemdraw-cdxml — 2D chemical structure and reaction-scheme drawing
• plotly-interactive-plots — interactive 2D scientific plots and dashboards

References

• 3Dmol.js documentation — GLViewer / GLModel API
• Rego & Koes, Bioinformatics 2015, 31(8):1322–1324 — 3Dmol.js: molecular visualization with WebGL
• GLViewer.animate — interval, loop, reps
• GLModel.vibrate — normal-mode animation from dx/dy/dz
• py3Dmol on PyPI — Python/Jupyter wrapper