PDB Converter

Convert database files (PDB) online for free


Drop or upload your .PDB file
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How to convert your PDB file

  1. Click the "Select File" button above, and choose your PDB file.
  2. You'll see a preview.
  3. Click the "Convert file to..." button to save your file in the format you want.

Convert PDB to another file type

The converter easily converts your PDB databases to various formats - free and online. No Microsoft Visual Studio or or other Developer software needed.

  • PDB to PDF
  • PDB to EPUB
  • PDB to HTM
  • PDB to AVS
  • PDB to NOL
  • PDB to QTL
  • PDB to PPM
  • PDB to RPNM
  • PDB to DOT
  • PDB to PIX
  • PDB to J2K
  • PDB to XLT

Convert a file to PDB

The converter also works in reverse, so you can convert other "Debug or Molecular Data" formats to PDB without using software like Microsoft Visual Studio or a similar tool.

  • IMG to PDB
  • MON to PDB
  • MTX to PDB
  • IPT to PDB
  • CIT to PDB
  • RTD to PDB
  • QTI to PDB
  • B_W to PDB
  • G3 to PDB
  • FL32 to PDB
  • GRO to PDB
  • J2C to PDB

About PDB files

The .PDB file extension is notoriously confusing because it represents entirely different, highly specialized formats depending on your industry. For software developers, it is a Program Database created by Microsoft Visual Studio to hold debugging symbols, memory addresses, and state information for compiled C++ or .NET applications. For scientists and researchers, it is a Protein Data Bank file, a standard text-based format used by the Worldwide Protein Data Bank to store 3D coordinates of biological macromolecules, opened with tools like PyMOL or AlphaFold2. Historically, .PDB was also widely used as a document and database format for legacy Palm OS mobile devices.

The main challenge with .PDB files is this extreme fragmentation. If you try to open a developer database in a text editor, it appears as an unreadable binary blob. If you are handling a molecular .PDB file, you are dealing with an ancient, rigidly structured text format created in the 1970s. It relies on exact column widths. If a single space is missing or misaligned, downstream molecular viewers will crash or completely misinterpret the atomic data. Meanwhile, legacy Palm OS documents are entirely obsolete, requiring specialized parsing to be read on modern screens.

If you need to archive or share molecular structures without breaking the layout, convert your .PDB to CIF (Crystallographic Information File) or XYZ. If you have an old Palm OS e-book, convert it to EPUB or PDF for reading on modern tablets. Developer debugging databases cannot be converted into standard text documents. Drag and drop your file to analyze and convert it - free, online, and without installing software right here on convert.guru.

Use Convert.Guru to open and convert your PDB file.

Users also converted PBD, DLL, PDP, PDBXML, PDBQT, CIF, MOL2, 3D, MOL, GRO, PRC, PDF and SDF files.


FAQ

If you want to convert PDB file to MOL2, FASTA, CIF, BAK, BACKUP, OLD, TMP, TEMP, ARC or ZIP, you can use Microsoft Visual Studio or similar software from the "Debugging Symbols & Molecular Structures" category. In the File menu, look for Save As… or Export….

To convert SNAPSHOT, OLD, RESTORE, ISO, COPY, VMDK, TMP, VHD, BAK, ARCHIVE or BACKUP files to PDB, try Microsoft Visual Studio or another comparable tool in the "Debugging Symbols & Molecular Structures" category.



The PDB Converter Story

The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our PDB converter.