Cryo-EM structure search · User guide

From density to
structural models.

CryoNet, your hub for
3D fitting review

Upload a cryo-EM density region, search structural databases for shape-similar proteins, and inspect local fitting results for candidate models. No registration or login is currently required.

Open Discovery Server Start reading

Inspect candidate fitting in density 01 · Visualize

Compare and download Top 100 candidates 02 · Evaluate

Upload a density map and choose a database 03 · Submit

Auto · 5 sec

Density region→DateDB search→Identified protein

Input.mrc, .map, or .ccp4; a segmented single-domain or single-chain region is recommended.

OutputNonredundant candidates, retrieval scores, fitting status, correlations, and downloadable structures.

InterpretationCandidates are structural-similarity results, not confirmed protein identities.

Before you start

Use a density region with complete boundaries. Preserve the correct voxel size, axes, and origin. Incorrect map headers affect both display and fitting. The current page states a maximum file size of 2 GB; follow the live server notice.

Use the top result as a candidateThe highest-ranked match is a useful starting point, but it is not automatically a confirmed identity. Review several leading results and compare their density fits before drawing a conclusion.

Database	Displayed size	Recommended use
CATH	5.7K domains / 78K structures	CATH domain-level identification
SCOPe	4.0K domains / 29K structures	SCOPe domain-level identification
PDB50	5.5K clusters / 520K structures	Broader PDB single-chain space
AFDB Cluster	30.0M chains / structures	AlphaFold DB predicted structures
MGnify-ESM30	36.9M chains / structures	Metagenomic predicted structures

Complete database menu — CATH, SCOPe, PDB50, AFDB Cluster, and MGnify-ESM30

Choosing a database

Selection ruleCATH and SCOPe target domain classifications; PDB50 covers clustered PDB chains; AFDB Cluster and MGnify-ESM30 extend the search to predicted structures. Database composition limits the possible answers, and a larger database is not automatically better.

Submit a job

Click Choose file under Cryo-EM density map.
Select the search Database.
Optionally enter a Target Name and notification Email.
Click Submit and keep the page open during upload.

Selected map and database — Select the file and database, then verify the form before submission

Use a Target NameIt helps distinguish experiments. If Email is blank, save the Job ID or result URL shown after submission.

Track progress

The upload bar shows a percentage. After job creation, the page displays status, a Stop button, and a Visualize and download results link. The blue string is the unique Job ID; clicking it opens Results Viewer in a new tab.

Fitting progress in Results Viewer — Track fitting progress with the status cards

Tested exampleexample.map was submitted to CATH as Job 260714_132941_66_d801bec214b2babeb09bbc08280f4d4a. It completed in about 338 seconds with 100/100 candidates fitted. Top 1 was 1e2y_G_0 (Z-score 4.15002; CATH 3.40.30.10). Runtime depends on the file, database, and queue.

Current timing issueCandidates may first show fitted while fit_corr is still being populated. If Corr remains “-” after completion, refresh the page.

Use Stop carefullyStop terminates the job. Click it only when the computation is no longer needed.

Results Viewer overview

The top cards show Job ID, Candidate Hits, Fitted Structures, Database, and Input Map. Updating or Job is running means the page is still refreshing. Retrieval can finish before all fitting jobs move from waiting/fitting to ready.

01Waiting

The candidate is queued for fitting.

02Fitting

The local model-to-density fit is running.

03Ready

The candidate can be opened in the viewer.

Results Viewer overview — Result status cards

Read both countersCandidate retrieval may already be complete while Fitted Structures is still increasing. Continue only when the candidate you need is ready.

Inspect the map and fitted structures

Click a ready candidate in the right-hand list to load it.
Map and Structure independently control visibility.
Contour Level changes the map isosurface in sigma units.
Drag to rotate, scroll to zoom, use Center to refocus, and Screenshot to save the current canvas.

3D map and fitted structure viewer — 3D viewer, candidate list, and display controls

Four Map / Structure combinations

The checkboxes only change visibility; they do not unload data. Changing candidates replaces the current structure but preserves the map. If Structure is off, a newly selected candidate also stays hidden.

Both hidden — With both controls off, the viewport is empty; re-enable either control to restore it

Contour Level

The range is −3.0 to 8.0 sigma, the step is 0.1, and the default is 2.0. Updates are rendered immediately. Lower values show more weak/background density; higher values retain only strong-density cores.

Center and Screenshot

Center refocuses with a 600 ms animation and prioritizes the map isosurface bounds. Even with Map hidden, it may frame the map rather than the structure alone. Screenshot exports the 3D canvas as <Job ID>_cryonet_discovery.png.

Centered view — Center refocuses the scene

Downloaded screenshot — The page Screenshot button exports a PNG

Native Mol* toolbar

Camera / Reset Zoom: fit the visible scene; its menu also includes Fit Visible Scene, Orient Axes, and Reset Axes.
Screenshot / State Snapshot: opens Mol*'s screenshot/state panel; this differs from the one-click page button.
Toggle Controls Panel: shows or hides Mol* controls.
Toggle Expanded Viewport: switches between embedded and expanded views.
Settings / Controls Info: opens rendering settings and interaction help.

Screenshot panel — Screenshot / State Snapshot

Settings and controls — Settings / Controls Info

Inspection tipCheck several contour levels. Confirm that the main density remains continuous, the model lies inside it, and no large model segment protrudes or major density remains unexplained.

Read and download candidates

Candidate cards display rank, name, status, Z-score, and Corr. The first fitted candidate opens automatically. A ready card and its table View button run the same loading action; controls are disabled before fitting finishes.

Top 100 Candidates table — Candidate table, View, Download, and TSV controls

Field	Confirmed behavior
Rank	Current candidate rank; numeric sorting.
Candidate	Main name and member tags link to RCSB; four are shown initially, +N more expands all, collapse closes them.
Domain	For CATH jobs, links to the corresponding superfamily.
AA length	120–1244 in this test; sortable.
Z-score	−1.27657–4.15002 in this test; sortable.
Fit corr	0.0220971–0.480273 in this test; sortable; “-” before population.
Fit status	fitted, fitting/running, waiting, or another state; sortable.
View	Loads a fitted model into the viewer.
Download	Opens the fitted PDB/mmCIF resource; it may appear in a new tab.

Expanded related candidates — +N more expands members

Only Rank, AA length, Z-score, Fit corr, and Fit status are sortable. The first click sorts ascending; the second reverses the order. Missing values remain last. Candidate, Domain, View, and Download are not sortable.

The three TSV files

File	Rows in this test	Contents
Unique hits TSV	100	Rank / Structrue IDs / Domain ID; one row per nonredundant domain/superfamily.
All hits TSV	78,481	Rank / Structrue ID / Domain ID / Detail information; every raw retrieval hit, without fitting data.
Fitting summary TSV	100	Eleven columns including structure path, status, AA length, Z-score, Fit corr, and fit seconds; all rows were fitted.

Download behavior and known issuesThe TSV controls open inline text in a new tab in some browsers. Structrue is the server's current header spelling. Candidate PDB links are also inline. The tested PDB content was valid, but the server reported application/vnd.palm; use Save As and retain the .pdb extension when necessary.

Result assessment checklist

Read the ranked list as converging evidence, then verify the fit against the density and your experimental context.

Do the leading hits indicate the same or related structural type?
Does the backbone sit within the main density, with compatible size and shape?
Within this job, does Fit Corr support the candidate?
Is the amino-acid length reasonable for the density region?
Do sample origin, complex composition, and known biology support the interpretation?

Three-way validation

A defensible interpretation should agree on all three signals.

Search consensus

Several leading hits converge on the same fold or structural family.

Density fit

The backbone remains inside continuous density across sensible contour levels.

Biological context

Length, sample origin, composition, and known function support the model.

Top 1 is not a confirmed identityIf leading hits disagree, fitting is poor, or the correct answer may be absent from the database, revise segmentation or database choice and use independent experimental evidence.

8. Troubleshooting

Submit is disabled

Select a supported .mrc, .map, or .ccp4 file. Refresh and select the file again if needed.

Upload stalls or reports an error

Check the network and file size, keep the page open, and retry. Record the time, browser, file size, and error if the problem persists.

Results remain waiting

Retrieval and per-candidate fitting are separate stages. Reopen the saved URL later; provide the Job ID to maintainers if nothing changes for an unusually long time.

The 3D view is blank

Click Center, enable Map, and adjust Contour Level. A structure is available only after its candidate becomes ready.

Fit Corr is “-”

Correlation may be populated after Complete / 100 fitted. Because polling can already have stopped, manually refresh the result page.

Download only opens a new tab

The server currently returns inline resources. Use Save As and preserve the .pdb/.cif/.mmcif or .tsv extension.

WebGL is unavailable

Mol* requires WebGL. Reopen the result in a hardware-accelerated browser. This does not mean retrieval or fitting failed.