OneTaskBy Tim King · Updated
Molecule Viewer Online
Open PDB and XYZ Files in 3D, Free, No Upload
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How the Molecule Viewer works
This molecule viewer online opens PDB and XYZ files in 3D. Drop a .pdb or .xyz file on this page and the molecule appears in 3D, coloured by element, with bonds worked out from the atom positions. Orbit it, switch between ball-and-stick, space-filling and stick styles, turn on element labels, read the formula, atom and bond counts, and download a PNG for a slide or a report. Six small molecules are built in so there is something to look at before you have a file, and nothing you open leaves your browser.
Molecule viewer online: opening a structure
Choose a molecule from the menu, or drag a file onto the drop zone or the viewport. XYZ files are the simplest format in chemistry: a line with the atom count, a comment line, then one atom per line as an element symbol and three coordinates in ångströms. They come out of quantum chemistry programs, Avogadro, ASE and most molecular editors. PDB files are the Protein Data Bank format used for proteins, nucleic acids and ligands; the viewer reads the ATOM and HETATM records of the first model, takes the element from the element column when it is filled in and from the atom name when it is not, and uses CONECT records for bonds when the file has them. Files up to about sixty thousand atoms open comfortably.
How bonds are found
Most files do not say which atoms are bonded, so the viewer works it out the same way molecular editors do: two atoms are joined when they are closer than about 115 percent of the sum of their covalent radii. That reproduces single, double and triple bonds as one stick each, which is what a structural view needs, and it copes with metals and unusual elements by falling back to a generous radius. A PDB file with a complete set of CONECT records is trusted instead. Hydrogen atoms in a crystal structure are sometimes placed slightly off, so an occasional missing H bond is the file, not the viewer.
Styles and colours
Ball and stick is the textbook view: small spheres joined by rods, easy to read for bond angles and ring shapes. Space filling draws each atom at its van der Waals radius, which shows the real shape and bulk of the molecule and is the right style for thinking about how it packs against a surface or a binding pocket. Sticks hides the spheres entirely, the usual choice for proteins and anything with hundreds of atoms where balls would hide the backbone. Atoms use the CPK colour convention: white hydrogen, grey carbon, blue nitrogen, red oxygen, yellow sulphur, orange phosphorus, green halogens. Element labels are drawn as floating symbols and switch themselves off above three hundred atoms, where they would be unreadable anyway.
Reading the statistics
The rail shows the molecular formula in Hill order (carbon, then hydrogen, then everything else alphabetically), the total and heavy-atom counts, the number of bonds found and the extent of the molecule along each axis in ångströms. For a protein, the heavy-atom count is the one to compare with the entry's header. The Download PNG button renders the current view on your own graphics card at preview, retina or 4K size with the chosen background.
Privacy
The file is read from disk into the page and never uploaded. Unpublished structures and proprietary compounds stay on your machine; once the page has loaded it works offline.
FAQ
Which file formats can I open?
PDB (.pdb or .ent) and XYZ (.xyz). If a file has no recognisable extension the page inspects the text and picks the parser itself. Multi-model PDB files, such as NMR ensembles, show the first model only. MOL, SDF and CIF are not read directly; Avogadro, Open Babel and RDKit can convert any of them to XYZ in a second.
Why are some bonds missing or wrong?
Bonds are inferred from distances, so a file with badly placed atoms, a structure with missing hydrogens or an unusual element outside the built-in radius table can gain or lose a stick. If a PDB file carries CONECT records for every atom those are used instead. The atoms themselves are always exactly where the file says; only the sticks are a guess.
Can it show a whole protein?
Yes, up to about sixty thousand atoms, which covers most single-chain entries and many complexes. Use the Sticks style, leave labels off and expect the bond detection to take a second or two on the largest files. It draws atoms and bonds only: there is no cartoon or ribbon view, no secondary structure colouring and no surface.
What do the colours mean?
They follow the CPK scheme that every chemistry package uses: hydrogen white, carbon grey, nitrogen blue, oxygen red, sulphur yellow, phosphorus orange, chlorine green, bromine dark red, iodine purple and common metals in their conventional tints. An element the table does not know is drawn pink so that it stands out rather than disappearing.
Are the coordinates in ångströms?
Both formats use ångströms by convention and the extent figures assume that. If an XYZ file was written in bohr or nanometres the molecule will look strangely large or small and the bond detection will fail; convert the units before opening it.
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