What is a .PDB file?
A PDB file is the classic record of a solved biological structure: one fixed-width line per atom giving its element, the residue and chain it belongs to and where it sits, preceded by header lines describing the experiment. The same extension is also the Microsoft Program Database of debug symbols and the Palm OS database.
- Did you know
- The fixed 80-column layout is inherited from punched cards, and its column limits are exactly why the Protein Data Bank had to move to mmCIF for large structures.
- Analyser handles .PDB alongside related formats such as .MOL, .SDF, .SD and more.
- In Analyser's format library, .PDB sits in the System & disk category.
- 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
- .PDB 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 .PDB file
- Drag a .PDB 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.