View MOL2 files in your browser
Tripos' molecule file, with atom types and charges, as docking apps hand it around. Open a MOL2 right here in 3D. Nothing leaves your device.
Or drop it anywhere on this page
What you'll see
Your molecule opens in 3D, a protein's chains as a cartoon and a small molecule's atoms as balls and sticks, with its parts beside it and what you pick on the other side.
- Turn, zoom and move it • Double click to center on a point
- Cartoon, balls and sticks or spacefill • By element, chain or residue
- Inspect an atom • Its residue, chain, charge and B-factor
- Export • PNG, GLB, USDZ, STL and OBJ
About MOL2
Tripos made MOL2 for SYBYL, its molecular modeling suite, and docking and simulation apps took it up: UCSF DOCK, GOLD, Open Babel and UCSF Chimera read and write it, and docking runs save their poses in it.
A MOL2 is text in sections that each start with @<TRIPOS>: MOLECULE names it and says how its charges were worked out, ATOM gives each atom's name, place, Tripos type, like C.ar for an aromatic carbon, residue and partial charge, and BOND each bond and its kind, aromatic and amide among them.
Filepeek reads it in your browser and puts each molecule on a page of its own, up to the first 200, in balls and sticks or spacefill. Click an atom for its type, partial charge and bonds, measure between atoms, and Export saves the view as PNG or the molecule as GLB, USDZ, STL or OBJ.
Tripos MOL2
.mol2
Format
- MIME type
- chemical/x-mol2
- Made by
- Tripos, for SYBYL
Inside the file
- Sections
- Each starts with @<TRIPOS>
- Atoms
- Place, Tripos type and partial charge
- Bonds
- Single, double, triple, aromatic or amide
- Markup
- Plain text
Opens in every browser
Filepeek opens MOL2 files in 3D in Chrome, Edge, Firefox and Safari. On their own, browsers download them or show them as text.
- YouChromeOpens through Filepeek
- YouEdgeOpens through Filepeek
- YouFirefoxOpens through Filepeek
- YouSafariOpens through Filepeek
Apps that open MOL2
- WindowsNo app built in opens it • UCSF ChimeraX, Avogadro and Open Babel read it
- MacNo app built in opens it • UCSF ChimeraX, Avogadro and Open Babel read it
- iPhone and iPadNo app built in opens it • Save it here as USDZ to see it in your room
- AndroidNo app built in opens it • Save it here as GLB for 3D apps
Questions
What do atom types like C.3 and N.ar mean?
They're Tripos' atom types, an element and how it's bonded: C.3 is a carbon with four single bonds and N.ar an aromatic nitrogen. Click an atom to see its type and partial charge.
Why are all my charges zero?
A MOL2 keeps the charges the app that saved it worked out, Gasteiger's or AM1-BCC's among them, and its MOLECULE section names which. NO_CHARGES means it has none. Show details says which kind the file has.
Can I step through a docking run's poses?
Yes. Each pose is a molecule of its own in the file, and the picker at the top steps through them in order.
Can I save it for 3D printing?
Yes. Choose Export, then Save as STL or OBJ for the style on show, or GLB for 3D apps and USDZ for an iPhone or iPad.