Where does the structure come from?

From the RCSB Protein Data Bank, the US site of the worldwide PDB archive, fetched at view time as the entry's PDB-format file, or its mmCIF file when no PDB-format file exists. The title, chains and ligand names in the summary are read from the entry's own header. The coordinates are not altered.

No. A file you open is read into your browser's memory, parsed there and drawn there; nothing leaves the device, and closing the page discards it. The only network request the viewer makes is the download of a PDB entry you ask for, and that request carries only the four-character ID.

What do the colors mean?

House: ink-gray protein with violet ligands. Chain: one hue per chain. Secondary structure: helix violet, sheet blue, coil gray. B-factor: a blue-to-violet gradient over each atom's temperature factor, scaled between the lowest and highest value in the loaded model, so the same color means different values in different entries.

How does the distance measurement work?

In measure mode, click two atoms: the viewer draws a line between their centers and labels its length in ångström, from the deposited coordinates. For scale, a carbon–carbon single bond is about 1.5 Å, a hydrogen bond between two heavy atoms 2.7 to 3.2 Å, and a salt bridge is usually counted within 4 Å.

Protein structure viewer — PDB in the browser

This viewer renders a macromolecular structure in the browser with 3Dmol.js, a WebGL library that runs entirely on your device: an entry is fetched from the RCSB Protein Data Bank by its four-character ID, or a local file is parsed in your browser and never uploaded anywhere. It is for anyone who wants to look at a target, an antibody or a peptide–receptor complex without installing software. Ligands, the HETATM records other than water, are drawn as sticks automatically.

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Fetching from the RCSB PDB…

Click two atoms to read the distance between their centers.

Title: —
Chains: —
Ligands: —
Atoms: —
Source: —

For reference and education. Nothing on this page is clinical guidance, a dose recommendation or an Epitorix performance figure; check every number against your own validated procedures.

How to read it

3Dmol.js 2.5

Representations and colors

Cartoon: The backbone trace: helices as ribbons, strands as arrows, the rest as tube. The default view.
Surface: The van der Waals surface at 60 % opacity over the cartoon, for the shape a ligand or a binder sees.
Sticks: Every heavy atom as a bond stick, for a close look at a site. Ligands are drawn as sticks in every mode, in violet under the house scheme.
House: Ink-gray protein, violet ligands: the site's palette, and the default.
Chain: One hue per chain, in the order the file lists them.
Secondary structure: Helix violet, sheet blue, coil gray, from the file's HELIX and SHEET records or 3Dmol.js's assignment when they are absent.
B-factor: Blue (lowest) to violet (highest) per atom, scaled within the loaded model. The B-factor is the crystallographic temperature factor; in cryo-EM entries the column holds whatever the depositors placed there.

Questions

files.rcsb.org

What the viewer does

Where does the structure come from?: From the RCSB Protein Data Bank, the US site of the worldwide PDB archive, fetched at view time as the entry's PDB-format file, or its mmCIF file when no PDB-format file exists. The title, chains and ligand names in the summary are read from the entry's own header. The coordinates are not altered.
Is my file uploaded?: No. A file you open is read into your browser's memory, parsed there and drawn there; nothing leaves the device, and closing the page discards it. The only network request the viewer makes is the download of a PDB entry you ask for, and that request carries only the four-character ID.
What do the colors mean?: House: ink-gray protein with violet ligands. Chain: one hue per chain. Secondary structure: helix violet, sheet blue, coil gray. B-factor: a blue-to-violet gradient over each atom's temperature factor, scaled between the lowest and highest value in the loaded model, so the same color means different values in different entries.
How does the distance measurement work?: In measure mode, click two atoms: the viewer draws a line between their centers and labels its length in ångström, from the deposited coordinates. For scale, a carbon–carbon single bond is about 1.5 Å, a hydrogen bond between two heavy atoms 2.7 to 3.2 Å, and a salt bridge is usually counted within 4 Å.

Sources and software

Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics 2015;31:1322–1324 (opens in a new tab) — the viewer library (BSD-3-Clause)
3Dmol.js — documentation and source (opens in a new tab) — representations, color schemes, selections
Berman HM et al. The Protein Data Bank. Nucleic Acids Res 2000;28:235–242 (opens in a new tab) — the archive
Burley SK et al. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models. Nucleic Acids Res 2023;51:D488–D508 (opens in a new tab) — RCSB PDB services and file downloads
wwPDB consortium. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res 2019;47:D520–D528 (opens in a new tab) — the archive's governance and CC0 data policy
RCSB PDB — file download service (files.rcsb.org) (opens in a new tab) — the download URLs the viewer uses

A viewer, not an analysis. It draws deposited coordinates as they are; it does not predict, dock, score or validate anything, and nothing here is an Epitorix performance figure. Structure data: RCSB PDB (CC0 1.0); software: 3Dmol.js (BSD-3-Clause).

Structures, in the browser.

Viewer

Representations and colors

What the viewer does

Sources and software

Viewer

Representations and colors

What the viewer does

The other six, open in the browser.