emdb-database SKILL.md skillA
emdb-database 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/emdb-database@git:20260522.6a6fd41Pins git:20260522.6a6fd41 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/structural-biology-drug-discovery/emdb-database/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260522.6a6fd41, committed May 22, 2026
- First version recorded
- Feb 18, 2026
- Size
- 19,861 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For atomic coordinates use pdb-database; for AlphaFold predictions use alphafold-database-access.
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
# EMDB Database
## Overview
The Electron Microscopy Data Bank (EMDB) at EBI archives 3D electron microscopy density maps — primarily cryo-EM and cryo-ET — for macromolecular assemblies (30,000+ entries: ribosomes, membrane proteins, viruses, large complexes). Access is split across two services:
- **EMDB Entry API** (`https://www.ebi.ac.uk/emdb/api/entry/{EMD-XXXXX}`) — the canonical per-entry JSON containing metadata, map header, fitted PDB list, and citation. Sub-endpoints like `/map`, `/fitted`, `/publications` do **not** exist — all those data live inside the single entry response.
- **EBI Search WS** (`https://www.ebi.ac.uk/ebisearch/ws/rest/emdb`) — the real keyword search backend (the bare `https://www.ebi.ac.uk/emdb/api/search/` endpoint ignores the query and just returns recent entries).
No authentication or API key is required.
## When to Use
- Finding cryo-EM density maps by keyword (e.g., "spike protein", "ribosome 70S")
- Fetching the download URL of a `.map.gz` density file for use in ChimeraX / PyMOL
- Identifying fitted PDB atomic models for an EMDB map (and the reverse)
- Retrieving entry metadata — resolution, reconstruction method, organism, sample
…Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/emdb-database@sha256:42bdba4bb5d2b18aThe line at the top of this page pins the label git:20260522.6a6fd41, 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_4al5cs72j43tclo5)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Feb 18, 2026 and May 22, 2026, about one every 46 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260522.6a6fd41 latest | 2026-05-22 | 6a6fd41 | 19,861 B | A | view · diff |
| git:20260428.81ea2d2 | 2026-04-28 | 81ea2d2 | 24,261 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 24,371 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (19861 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
- pass: No script tag
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_4al5cs72j43tclo5 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/emdb-database GET https://markdownregistry.com/api/v1/blob/42bdba4bb5d2b18a01195462d0503de6ca18ec3b1544c205870e709390bfcf20
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.