Protein Structure Viewer

Protein Structure Viewer Compare, annotate, and publish predicted and experimental structures — entirely in your browser

Add structures or AlphaFold result ZIPs Drop files anywhere on this page, or choose PDB, CIF/mmCIF, JSON, CSV, A3M and ZIP files Multiple ZIPsLocal processingNo upload

Fetching contacts files.rcsb.org or alphafold.ebi.ac.uk. Files you open locally are never sent anywhere.

Current model

No structure loaded yetDrop a PDB, CIF, or AlphaFold ZIP anywhere on this page, or fetch an ID above

0 structures Mean pLDDT — Ready

Source Find models View mode Model order Interval 2.0 s

Load one or more structures to begin.

Click a residue in the viewer or in the sequence strip to inspect it.

Go to

Residue label Label every residue Label style

Selection model Chain Residues Action Highlight color

Near Chain Within (Å)

Sequence motif Regular expression over one-letter codes; X stands for unknown residues.

Domains

Name a region, give it a colour, and choose how far it applies: this model only, every model from the same source (an AlphaFold run), or every loaded model. Colour by annotated domains paints them and lists them by name in the legend.

Domain name Chain Residues Colour Applies to

Per-residue data

Map your own numbers onto the structure — conservation, deep mutational scores, ΔΔG, coverage. A table with residue and value columns (chain optional) as CSV or TSV, chosen or pasted. Colour by per-residue data paints the values with a gradient legend, and the sequence strip follows.

Table file Or paste Name Colour scale Applies to No per-residue data loaded.

Measurement Measurement mode is off.

Figure annotations

Arrows, lines, markers and callouts are anchored to atoms, so they follow rotation and alignment and appear in PNG exports, comparison panels, and the shared report.

Tool Text Colour Size 1× Dashed Pick a tool, start drawing, then click atoms in the main viewer.

Screen text Corner

Alignment reference Residue mapping

Synchronized multi-view Camera sync Primary panel

Every panel follows the others as you drag, spin, or rock. Rotation only keeps each model framed on its own centre, which suits assemblies of different size. Rotation and zoom locks the cameras completely, which suits superposed models of the same target after Align visible.

Interface contact map

Chain against chain Atoms Cutoff (Å)

Show a model with two or more chains.

MSAColour byNo alignment loaded. AlphaFold 3 archives carry one per entity; an .a3m can also be added on its own.

Model	Mean pLDDT	pTM	ipTM	Ranking score	Rank	Clash

PAE domains

Residues whose predicted aligned error to one another is low are placed together in the prediction. Ten-residue segments are merged greedily while the mean PAE between groups stays below the cutoff. This reads the PAE matrix; it is not a structural domain assignment, and it says nothing about whether the placement is right.

PAE cutoff Show a model with a PAE matrix, then find its domains.

Ligand sites

For each ligand or ion of the current model: the residues with a heavy atom within the cutoff, their mean pLDDT, and — when the PAE matrix carries ligand tokens (AlphaFold 3) — the mean predicted aligned error between the ligand and its site. A low site pLDDT or a high ligand–site PAE says the pose is not to be trusted, whatever it looks like.

Contact cutoff (Å) Show a model with ligands or ions.

Interfaces

Geometry of the model as loaded: inter-chain heavy-atom contacts and buried surface area (Shrake–Rupley, 1.4 Å probe, 92 points per atom). A predicted interface is a hypothesis about an interaction, not evidence of one — read it next to the chain-pair ipTM and PAE above.

Model Contact cutoff 4.0 Å Highlight colour

Image size Scale Output Journal preset Figure width Custom width (mm) Aspect Resolution Text size Figure font Scale bar

Composite figure PAE heatmap pLDDT profile Contact map Columns Colour legend on exports Video length

Report contents PAE in report Embed 3Dmol.js for offline use Load models to estimate the report size.

Publication checklist

View name Caption Panel columns

Provenance and reproducible scene

Figure or project titleModel source or runMethod and versionNotes

Restore scene JSON

Open session fileA session file carries the models themselves, so it reopens with no other files. Scene JSON is the light alternative that expects the original files.

Getting structures in

Drop .pdb, .cif, .mmcif, or whole AlphaFold result .zip archives anywhere on the page.
Add AlphaFold *_confidences.json, *_summary_confidences.json, ranking_debug.json, or ranking_scores.csv to attach pTM, ipTM, ranking scores, and PAE to matching models.
Type an identifier to fetch it: a four-character PDB ID (1ubq), a UniProt accession (P69905), or an AlphaFold DB name (AF-P0DTC2-F1).

In the 3D view

Drag to rotate, scroll to zoom, right-drag or two-finger drag to pan.
Click any atom to inspect its residue, chain, and pLDDT, and to place a label.
Use Figure annotations in the Annotate tab to draw arrows, lines, residue markers, and text callouts by clicking atoms, and to add corner titles. They follow rotation and alignment and are included in PNG exports and reports.
Turn on Synchronized multi-view in the Compare tab to show up to six models in linked viewports. Dragging, spinning, or rocking any one of them moves them all.

Keyboard

`←` `→`	Previous / next model
`C`	Start or pause automatic cycling
`F`	Fit every panel to what it displays
`S`	Start or stop spinning
`X` `Y` `Z`	Rotate 90° about that axis (`Shift` reverses); `Shift` + `R` resets orientation
`Shift` + `F`	Toggle full screen
`1` – `6`	Jump to a tool tab
`Ctrl`/`⌘` + `Z`	Undo the last label, selection, measurement or annotation change; add `Shift` to redo
`?`	Open this help
`Esc`	Close help, leave full screen, stop measuring

Your work is kept

The open models, annotations, domains, views and settings are saved in this browser a moment after every change. Reopening the page offers to restore them; Forget it discards the copy. Nothing leaves the browser. For anything you must keep, download scene JSON or a report.

How to cite

Cite the viewer and the rendering library it builds on. Each GitHub release is archived on Zenodo with its own DOI; the repository's CITATION.cff carries the current metadata.

Awuah, M. B. (2026). Protein Structure Viewer, version [software]. github.com/mbaffour/protein-structure-viewer.
Rego, N. & Koes, D. (2015). 3Dmol.js: molecular visualization with WebGL. Bioinformatics 31(8), 1322–1324. doi:10.1093/bioinformatics/btu829.

Reading the numbers

pLDDT is per-residue local confidence. High pLDDT does not mean the relative placement of chains is right.
PAE and ipTM are what to read for interfaces and domain placement in complexes.
RMSD from the Compare tab is a visual-comparison aid. Always report the alignment method, chain mapping, and aligned Cα count alongside it.

Tips for figures and reviewers

Publish → Write methods text drafts a Methods paragraph stating exactly how the numbers on screen were computed (superposition, RMSD, RMSF, domains, contacts, dimensions, colour scales); every definition is cross-checked against Biopython in the repository's VALIDATION.md.
Confidence → Colour by MSA reads the alignment inside an AlphaFold 3 archive (or an .a3m you add) and colours matching chains by conservation, identity to the query or coverage; the legend, exports and methods text follow.
Publish → Download composite figure stitches the 3D view with the PAE heatmap, the pLDDT profile and the contact map into one lettered figure at print size, each panel rendered at output resolution.
The Publication checklist at the foot of the Publish tab lists what a journal or reviewer would flag about the current figure — no physical size, low resolution, small text, colour-blind-unsafe colours, missing legend, scale bar in perspective, unsuperposed models, no title — with one-click fixes.
Compare → Interface contact map draws every residue pair of two chains within a cutoff, closer pairs darker; hover reads the pair, a click selects both residues, Highlight interface colours the interface, and the map and pair list download as PNG and CSV. Annotate → Label style switches every label between boxed and plain text.
Appearance → Outline draws a silhouette line around every element (thin for most figures, bold for small panels) and Depth cueing fades the far side; both apply to panels and exports. In the composition table, Faded blends a chain into the background to spotlight the others. Publish → Journal preset sets width, resolution, text size and font from a journal's figure guide, and Download one panel per model renders every model from the same camera into one lettered figure.
The layout button in the header (panel icon) switches between the side-panel workspace, where the 3D view stays pinned while you work in the scrolling tool panel, and the stacked layout. Drag the divider between them to give tables more room; double-click it to reset. Screens narrower than 1100 px always stack.
Publish → Save session file writes one ZIP with the models, confidence data, alignment, annotations, domains, views and settings; open it later with Open session file or by dropping it on the page, on any computer, with no other files. Scene JSON remains the light option that expects the original files.
Large AlphaFold 3 archives open whole: the confidence files are scanned byte by byte, the unused contact matrix is skipped and the PAE is kept compactly, so a five-model, 4 400-token assembly stays well under a gigabyte of memory.
Colour by pLDDT confidence and switch to orthographic projection for publication panels; perspective exaggerates whatever is closest to the camera.
Run Align visible, then enable multi-view with Rotation and zoom to inspect a superposition panel by panel. The shared report carries the aligned coordinates.
Save named views with captions in Publish: they become lettered figure panels, a caption file, and a guided tour inside the report.
Rename a model in the Models list to give it the name a caption should carry; file names stay as identifiers underneath.
Download comparison PNG stitches the current panels into one lettered figure at the export size you chose; the SVG variants keep labels, arrows, captions, and the legend as editable vector layers over the rendered molecule.
Every residue label and annotation is editable in its list row — text, colour, and size — and can be nudged with the arrow buttons; it moves in screen space and stays put when the model turns. Callouts also take a leader length.
Interfaces in the Confidence tab counts inter-chain contacts and buried surface area for a model, and can highlight the interface residues. Read it next to ipTM and PAE; a predicted contact is not an observed one.
Tick Embed 3Dmol.js for offline use before sharing a report that must open without internet; drop the PAE detail to Compact or Omit to keep it small.
Keep Report contents on Models currently shown for a small file reviewers can open on a laptop; switch to Every loaded model for an archive.

Everything runs locally. Structure files you open are read in the browser and are never uploaded.