molecular-visualization-3dmol SKILL.md skillB
molecular-visualization-3dmol from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/molecular-visualization-3dmol@git:20260815.55f9733Pins git:20260815.55f9733 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- B, 16 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/data-visualization/molecular-visualization-3dmol/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260815.55f9733, committed Aug 15, 2026
- First version recorded
- Aug 15, 2026
- Size
- 12,837 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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 …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/molecular-visualization-3dmol@sha256:fdd9d04fa9752ad8The line at the top of this page pins the label git:20260815.55f9733, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_4bjox4e5ssdedvgs)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, all committed on Aug 15, 2026.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260815.55f9733 latest | 2026-08-15 | 55f9733 | 12,837 B | B | view · diff |
| git:20260815.8947036 | 2026-08-15 | 8947036 | 12,941 B | B | view |
Audit of the latest version
- fail: No script tag (matched: <script)
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (12837 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
Starting a new one? Use a template for SKILL.md on mdpantry, which passes every one of these checks and says what to change in it.
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_4bjox4e5ssdedvgs GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/molecular-visualization-3dmol GET https://markdownregistry.com/api/v1/blob/fdd9d04fa9752ad8807c56d3165cc4d185d7c5b6d93a6134cca0c4b5bd23a7ff
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.