Protein Data Bank 3.3
Writableother
The Protein Data Bank file format was developed as a human readable, standardised way to describe the 3D structures of molecules. The file is limited to 80 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates. It was developed in 1972, and has gone through various versions, the last one being version 3.3 (defined here), which was released in 2012. The file was succeeded by the .mmCIF format in 2014.
Identify it
| Extensions | .pdb.ent.brk |
|---|---|
| MIME types | chemical/x-pdb |
| PRONOM | fmt/2009 |
| Wikidata | Q7251429Q128035062 |
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Open it
- ImageMagickOpen source
- AvogadroOpen source
- BALLOpen source
- bioSyntaxOpen source
- BlenderOpen source
- Cn3DOpen source
- CootOpen source
- GabeditOpen source
- GENtleOpen source
- GeworkbenchOpen source
- JmolOpen source
- MolekelOpen source
- OpenBabelOpen source
- Q1036510Open source
- RasMolOpen source
- UGENEOpen source
- VisItOpen source
Convert it
| To | With | Fidelity | Command and losses |
|---|---|---|---|
| Portable Network Graphics | ImageMagick | Lossless | convert in.pdb out.pngPixels kept; some metadata, colour profiles or layers may be dropped. |
| Tagged Image File Format | ImageMagick | Lossless | convert in.pdb out.tifPixels kept; some metadata, colour profiles or layers may be dropped. |
| GIF 89a | ImageMagick | Lossy | convert in.pdb out.gifReduced to 256 colours. |
| JPEG File Interchange Format 1.02 | ImageMagick | Lossy | convert in.pdb out.jpgLossy compression. |
| WebP | ImageMagick | Lossy | convert in.pdb out.webpLossy compression. |
Sources
From Converters (FFmpeg, ImageMagick, Pandoc, LibreOffice), Just Solve the File Format Problem (File Formats Wiki), PRONOM, Wikidata. Updated 2026-10-24.