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.
SkillScore100Maintained
Automatic
◆Research pack
Last verified 8/23/2026
What it changes
Passed 22 of 22 test cases with the skill, and 12 of 22 without it.
Without skill55%
With skill100%
Checks it passed that the model alone missed
The script reads the valueOf_ key from the organism dictionary.
The loop terminates when collected items equal or exceed hitCount.
The code checks for author or author_order keys under citation_type.
and 10 more in the full report
10 fixed12 passed either way0 still failing0 broke
Pass-rate lift
+45 pp
Tokens
+210%
Agent turns
0%
Response time
-29%
Model gemini-3.6-flashMeasured 8/23/2026v122 of 22 cases passed with skill
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 10 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 10
Prompt
Write a Python snippet to extract the natural source organism name from an EMDB entry JSON payload.
What was checked, without and with the skill
Checked
Without skill
With skill
The script navigates through sample.supramolecule_list.supramolecule to access natural_source.
Missed
Passed
The script reads the valueOf_ key from the organism dictionary.
Missed
Passed
case-10 · gemini-3.6-flash · 8/23/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md456 linessingle file
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)