What is a .XYZ file?
XYZ is the plainest structure format there is: a count, a comment line, then one line per atom giving its element and three numbers. No bonds, no cell, no metadata.
- Did you know
- Because it records no bonds at all, anything drawing an XYZ file has to work out which atoms are bonded from how close together they are.
- The XYZ format originated in the XMol visualisation software developed at the Minnesota Supercomputer Center, affiliated with the University of Minnesota.
- An XYZ file starts with a line giving the number of atoms, then a free-text comment line, before listing each atom’s element and coordinates.
- 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
- .XYZ 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 .XYZ file
- Drag a .XYZ 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.