Free Online Molecule Viewer (No Signup)
Also opens DWG, DXF, STEP, IGES, IFC, SKP, STL, OBJ, GLB, FBX, 3DM and other 3D/CAD files. Drop any file on the viewer.
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Describe a compound, a protein or a crystal. The AI finds it in PubChem or the Protein Data Bank, or builds it, and opens it here.
Create a model with AI
Describe what you need, or add a photo, and AI builds it at real size in the viewer. Ask for changes in the chat, then export it. Free, with your own Anthropic or OpenAI key.
Open the AI GeneratorWhat Is a Molecule File?
Every molecular file stores the same core: a list of atoms, each with its element and its position in ångströms (one ten-billionth of a metre). Formats differ in what they add. Structures of proteins and nucleic acids (PDB and mmCIF) group atoms into residues and chains and record helices and strands; small-molecule formats (SDF and MOL, MOL2) list each bond with its order; a crystallography CIF gives the unit cell; a GROMACS .gro file is a snapshot of a simulation box; and a chemistry .xyz file is just the element and coordinates of each atom.
This viewer reads all of them and picks the drawing that suits the molecule. Proteins and nucleic acids open as a cartoon of their chains with ligands as ball and stick; small molecules open as ball and stick with double, triple and aromatic bonds drawn as parallel cylinders. Atoms are coloured by element in the familiar Jmol colours, and a Space filling layer shows every atom at its van der Waals radius.
Each format has its own page with the details: PDB viewer, CIF viewer, SDF and MOL viewer, MOL2 viewer and GRO viewer.
Who Uses Molecule Files?
Structural biologists, biochemists and medicinal chemists checking a structure without opening PyMOL, ChimeraX or Avogadro; students and teachers in biology and chemistry classes; science writers and illustrators; and designers, architects and exhibition makers who want a real protein or crystal for a render, a 3D print, a sculpture or a piece of a building.
Common Use Cases
- Open a protein downloaded from the RCSB Protein Data Bank and turn it in 3D
- Look at a compound from PubChem or ChEMBL as ball and stick
- Check a crystal structure from the Crystallography Open Database with its unit cell
- Share a structure with a class, a colleague or a client as a link that opens in any browser
- Export a molecule as STL or 3MF for a 3D print, or as GLB, FBX or USDZ for Blender, a game engine or AR
Features
Opens Every Common Format
PDB, PDBQT, PQR, mmCIF, CIF, SDF, MOL, MOL2, GRO and chemistry XYZ.
Cartoon of Every Chain
Helices and strands as ribbons from the file, or worked out from the Cα trace; one chain coloured blue to red, several chains each in its own colour.
DNA and RNA
Nucleic acids as a tube along the backbone with the bases as sticks.
Ligands as Ball and Stick
Bound ligands, cofactors and ions drawn as ball and stick, coloured by element.
Ball and Stick
Atoms coloured by element, with double, triple and aromatic bonds drawn as parallel cylinders.
Space Filling
A layer with every atom at its van der Waals radius.
Export to GLB, STL or USDZ
Save the structure as GLB, glTF, OBJ, STL, 3MF, PLY, FBX or USDZ for a render, a 3D print or AR, or the view as a PNG.
Measure in Ångströms
Click two atoms to measure the distance between them, in Å.
View in VR
On a headset browser the molecule stands on a table in front of you.
Nothing Is Uploaded
The file is read entirely in your browser. No account, no upload, no copy on a server.
Share and Embed
Send a link that opens the molecule in any browser, or drop the viewer into your own page with one iframe.
Compatibility & Format Notes
Files that open: PDB (.pdb, .ent) with its AutoDock PDBQT (.pdbqt) and APBS PQR (.pqr) variants; PDBx/mmCIF and small-molecule CIF (.cif, .mmcif, .mcif); MDL molfiles and SD files in V2000 and V3000 (.mol, .sdf, .sd); Tripos MOL2 (.mol2, .ml2); GROMACS structures (.gro); and chemistry XYZ (.xyz). An .xyz file that is a molecule is told apart from an .xyz point cloud by its content.
Proteins open as a cartoon: helices and strands as ribbons, taken from the file’s secondary-structure records when it has them and worked out from the Cα trace when it does not, with loops as a round tube. A single chain is coloured along its sequence from blue at the start to red at the end; when there are several chains, each gets its own colour. DNA and RNA open as a tube along the backbone with the bases as sticks. Ligands are drawn as ball and stick, coloured by element (carbon grey, oxygen red, nitrogen blue, sulfur yellow, in the Jmol colours).
Small molecules open as ball and stick, with a Space filling layer beside it. An SD or MOL2 file that holds many molecules opens with one layer per molecule. Only the first model of an NMR ensemble and the first frame of a multi-frame XYZ file are drawn.
Coordinates are read in ångströms (Å) and kept at that scale, so the measuring tool reads distances in Å. Bonds are taken from the file where it lists them and worked out from covalent radii for the rest. Very large structures, such as a whole virus capsid with millions of atoms, open with the cartoon and with their atoms drawn as points so the browser keeps up.
Embed on Your Website
Add this viewer to your own site with a single line of HTML. Click Embed in the toolbar to generate an embed code, or use the snippet below with your own file URL.
Your Files Stay on Your Computer
Your Molecule files are parsed entirely in your browser. Nothing is uploaded, stored, or shared unless you explicitly click the Share button. Shared files are hosted for 90 days then deleted.
Frequently Asked Questions
▶Which molecular file formats open?
PDB, PDBQT and PQR; PDBx/mmCIF and crystallography CIF; MDL MOL and SDF (V2000 and V3000); Tripos MOL2; GROMACS GRO; and chemistry XYZ. The format is recognised from the file’s content as well as its extension.
▶How is the molecule drawn?
Proteins and nucleic acids as a cartoon of their chains, with ligands as ball and stick. Small molecules as ball and stick, with double, triple and aromatic bonds as parallel cylinders. Every atom is coloured by element, and the Layers panel switches on sticks for every atom, hydrogens, water, space filling and the unit cell.
▶Do I need PyMOL, ChimeraX or other chemistry software?
No. The file is read and drawn in your browser on any computer, tablet or phone. Nothing is installed and nothing is uploaded.
▶What units are the coordinates in?
Ångströms, as the files store them (a GROMACS file in nanometres is converted to ångströms). The measuring tool reads distances in Å, so a carbon-carbon single bond measures about 1.5.
▶Can I 3D print the molecule?
Yes. Export STL or 3MF and open it in your slicer. Thin cartoon ribbons and sticks are fragile at small sizes, so for a sturdy print switch on Space filling (or ball and stick for a small molecule) before exporting, and scale the model up in the slicer: one ångström in the file is one unit in the export.
▶Can I look at it in VR?
Yes. On a headset browser (Meta Quest, Apple Vision Pro, Pico) click VR in the toolbar and the molecule stands on a table in front of you, scaled to a size you can walk around and lean into.
▶Is this molecule viewer really free?
Yes, completely free. No signup, no watermarks, no file size limits on the viewer (the optional share-link feature has a 100 MB upload cap). Built by Innerscene as a tool for architects, engineers, and designers.
▶Are my files uploaded to a server?
No. All parsing, rendering, and conversion runs in your browser: nothing is uploaded, stored, or transmitted by default. The Share button is the only feature that uploads a file, and only when you explicitly click it.
▶Can I convert to another format?
Yes. Click Export in the toolbar to save the structure as GLB, glTF, OBJ, STL, 3MF, PLY, FBX or USDZ, or the view as a PNG picture. The export carries the layers you have switched on, so turn on Space filling or Polymer atoms first if you want them in the file. There is no PDB or SDF writer: the exports are 3D models of the picture you see.
▶Can I embed this viewer on my own site?
Yes. Click Embed in the toolbar to generate a one-line <iframe> snippet you can paste into any HTML page. You can choose whether the embed shows the viewer’s toolbar.