3D Molecular Structure Viewer
Turn any molecule in your hands: search PubChem and the Protein Data Bank, open your own structure files, measure bond lengths and angles, and see VSEPR shapes with their lone pairs.
At a glance
- Finds any compound in PubChem by name, SMILES string or CID and shows its 3D shape, and any entry of the Protein Data Bank by its four-character ID.
- Opens PDB, mmCIF, SDF/MOL, MOL2, XYZ, PQR and GRO files on your device — dropped, chosen or pasted — without uploading them.
- Shows molecules as ball and stick, sticks, space-filling or wire, and proteins and DNA as a cartoon with their ligands, coloured by element (CPK), chain, helix and sheet, or rainbow.
- Measures distances in ångströms, bond angles and torsion angles between any atoms you click.
- 36 molecules built in — from water and methane to caffeine, ATP and cholesterol — and 12 VSEPR shapes with their lone pairs, from linear CO₂ to square planar XeF₄.
- Lists the formula in Hill order, the molar mass from IUPAC (CIAAW) atomic weights, and for proteins the chains, residues, ligands, method and resolution. Drawn with 3Dmol.js (WebGL).
Step by step
How to view a molecule in 3D
- 1
Find the molecule
Type a name, SMILES, PubChem CID or PDB ID and press Show — or choose one from the library, or Open file.
- 2
Turn and zoom
Drag to turn it, scroll or pinch to zoom, or use the buttons under the view. Spin sets it turning on its own.
- 3
Change the style
Choose Ball and stick, Sticks, Space-filling or Wire — or Cartoon for proteins — and switch hydrogens and labels on or off.
- 4
Measure
Pick Distance, Angle or Torsion and click the atoms in the view.
- 5
Save or share
Use Picture for a PNG, download the file, or Copy link to send the same molecule to someone else.
Features
Everything you need, nothing you don’t
Search like a chemist
Type “aspirin”, a SMILES string such as CC(=O)Oc1ccccc1C(=O)O, a PubChem CID such as 2244, or a PDB ID such as 1CRN — the box works out which it is.
Your files stay yours
Structure files you open are read in your browser and never uploaded. Only searches go to PubChem or the Protein Data Bank.
Measure the geometry
Click two atoms for a bond length, three for an angle, four for a torsion. The values are drawn into the 3D view and listed beside it.
VSEPR you can turn around
Twelve shapes from linear to octahedral, with lone pairs shown as purple clouds — real molecules where PubChem has them, ideal geometry otherwise.
Proteins and DNA
Cartoons of helices and sheets, ligands in ball and stick, optional water and a molecular surface, with chains, residues, method and resolution listed.
Ready for slides and worksheets
Save a picture with a white, black or page background, download the structure as its original file or as XYZ, and copy a link that opens the same molecule.
Ways to show a molecule
| Style | What it shows | Good for |
|---|---|---|
| Ball and stick | atoms as small balls, bonds as sticks | seeing bonds and angles |
| Sticks | bonds only, coloured by atom | crowded molecules |
| Space-filling | atoms at their van der Waals size | the real shape and bulk of a molecule |
| Wire | thin lines for bonds | very large structures |
| Cartoon | the protein backbone as helices, sheets and loops | proteins and DNA |
What the colours mean
Atoms are coloured with the CPK convention, in the shades used by Jmol and most viewers:
| Element | Colour | Element | Colour |
|---|---|---|---|
| Hydrogen | white | Sulfur | yellow |
| Carbon | grey | Phosphorus | orange |
| Nitrogen | blue | Fluorine and chlorine | green |
| Oxygen | red | Bromine | dark red |
VSEPR shapes in the library
| Shape | Example | Electron pairs (bonding + lone) | Angles |
|---|---|---|---|
| Linear | CO₂, XeF₂ | 2 + 0, or 2 + 3 | 180° |
| Trigonal planar | BF₃ | 3 + 0 | 120° |
| Tetrahedral | CH₄ | 4 + 0 | 109.5° |
| Trigonal pyramidal | NH₃ | 3 + 1 | about 107° |
| Bent | H₂O | 2 + 2 | about 104.5° |
| Trigonal bipyramidal | PCl₅ | 5 + 0 | 90° and 120° |
| Seesaw | SF₄ | 4 + 1 | ideally 90°, 120°, 180° |
| T-shaped | ClF₃ | 3 + 2 | ideally 90° |
| Octahedral | SF₆ | 6 + 0 | 90° |
| Square pyramidal | BrF₅ | 5 + 1 | ideally 90° |
| Square planar | XeF₄ | 4 + 2 | 90° |
FAQ
Frequently asked questions
Which file formats can I open?
Where do the 3D shapes of small molecules come from?
Why are there no hydrogen atoms in my protein?
How do I measure a bond angle?
What do the purple clouds mean?
Can I use the pictures in my slides or homework?
Does it work on a phone?
What is sent over the internet?
Keep going
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