What is a .MOL file?
A MOL file is a connection table: a block of atoms with their coordinates, then a block saying which pairs are bonded and how. That explicit bond list is what separates it from a bare coordinate file, and it is why a molecule drawn from one looks the way a chemist expects.
- Did you know
- The MDL Molfile dates from the early 1980s and its counts line is still fixed-width, which is why an atom count above 999 needs the newer V3000 variant of the same format.
- The Molfile was introduced by MDL Information Systems in 1979 and centres on a connection table describing a molecule’s atoms and bonds.
- Its widely used V2000 layout caps a structure at 999 atoms, so larger molecules need the extended V3000 variant.
- What Analyser reads
- Open chemical structures and see the molecule: MOL and SDF connection tables, MOL2, plain XYZ coordinates, Protein Data Bank entries and mmCIF/CIF crystallographic files, all drawn in an interactive 3D viewer you can rotate, zoom and restyle. Small molecules come up as ball-and-stick with the standard element colours; proteins and nucleic acids get a cartoon instead, drawing each chain as a ribbon along its backbone with helices and sheets picked out and any bound ligand still shown as sticks - which is the only way a structure of tens of thousands of atoms is readable at all. Alongside the picture, the composition is worked out from the atoms actually present rather than from any label in the file: molecular formula in Hill notation, molecular weight, net charge, element counts, and for a macromolecule the chain, residue and secondary-structure counts plus every non-polymer group - bound drugs, cofactors, metal ions and crystallisation buffer. PDB headers give up the entry ID, title, experimental method and resolution; an SDF is stepped through record by record with each molecule's tagged data fields read out.
- Depth of analysis
- .MOL is an identification-grade format: Analyser recognises it from its bytes and decodes the header metadata it carries, rather than opening it in a full viewer. Formats that do get a full viewer are marked "Full" on the formats page.
- Open a .MOL file
- Drag a .MOL file onto the Analyser home page (or tap to pick one). It is identified entirely in your browser - nothing is uploaded, there is no account, and it works offline once installed.