molecular-visualization-3dmol

molecular-visualization-3dmol is a skill for Claude Code from jaechang-hits/SciAgent-Skills. It costs 169 tokens per session (3,591 once invoked), scanned A, original, no licence file.

A browser-based 3D viewer for molecular structures, built with 3Dmol.js and delivered as a self-contained HTML file. It can display formats such as PDB, SDF, XYZ, MOL2, and cube files.

In plain words
What is it for?
Use it to show molecules as sticks, spheres, cartoons, lines, or surfaces; play structure trajectories; and animate vibrational normal modes from per-atom movements.
Why use it?
It avoids requiring a separate molecular-visualization application to inspect structures. It also provides consistent styling and animation controls in a shareable HTML file.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the sciagent-skills plugin — 146 skills shipped together

Good fit Use it to show molecules as sticks, spheres, cartoons, lines, or surfaces; play structure trajectories; and animate vibrational normal modes from per-atom movements.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add jaechang-hits/SciAgent-Skills --skill molecular-visualization-3dmol
Clone the repo
git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills

Made for: Claude Code.

Or install sciagent-skills, the plugin that ships this one along with the rest of its 146 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for molecular-visualization-3dmol

README.md
[![agentmods](https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol/github.svg)](https://agentmods.dev/skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol)
Your own site
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for molecular-visualization-3dmol

Your own site · 80×15
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/molecular-visualization-3dmol.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 169 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,591 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00169 $0.03591
Opus 5 $0.00084 $0.01795
Sonnet 5 $0.00034 $0.00718
Haiku 4.5 $0.00017 $0.00359

Measured 13d ago against content hash fdd9d04fa975, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

molecular-visualization-3dmol scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 13d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/mol_viewer.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/data-visualization/molecular-visualization-3dmol/SKILL.md · 263 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 13d ago First seen · 263 lines · 169 tokens per session scan A fdd9d04fa975

Subscribe to this mod's changes

molecular-visualization-3dmol is a skill published in the GitHub repository jaechang-hits/SciAgent-Skills (362 stars, last pushed 14d ago), with no licence file. It adds 169 tokens to every session and 3,591 once invoked, about $0.0008 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.