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PDB to CSV

Universal Format Converter

Convert between CSV, TSV, JSON, and Excel. Supports multiple files, primary data, and batch operations.

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About PDB to CSV

Convert Protein Data Bank (PDB) atomic coordinate files into CSV rows with atom name, residue, chain and X/Y/Z coordinates.

PDB files describe the 3D atomic structure of proteins and other macromolecules using a fixed-width text layout where each ATOM or HETATM line packs atom name, residue, chain, sequence number and X/Y/Z coordinates into exact character columns — a format built for programs, not people.

This tool reads those fixed column positions precisely, per the official PDB specification, and lays each atom out as a proper CSV row with serial number, atom name, residue name, chain ID, coordinates, occupancy, temperature factor and element clearly separated.

That turns a wall of cryptic fixed-width text into something you can sort by chain, filter by residue, or plot coordinates from directly in a spreadsheet, without needing PyMOL or a structural biology toolkit installed.

It also serializes CSV data back into padded, spec-compliant PDB lines, so you can round-trip a filtered or edited atom list back into a structure file.

Category: Scientific Formats

Common Use Cases

  • Reviewing atomic coordinates in a spreadsheet
  • Feeding structure data into custom analysis scripts

Key Features

  • Reads ATOM/HETATM fixed-width columns at their exact spec-defined character positions
  • Outputs serial number, atom name, residue, chain, X/Y/Z, occupancy and temperature factor as columns
  • Serializes edited CSV rows back into padded, spec-compliant PDB lines
  • Runs client-side, so no PyMOL or structural biology toolkit install is required

The PDB to CSV tool is compatible with: Structural Biology Tools, PyMOL, RCSB PDB.

Pull a structure's atomic coordinates into CSV here for filtering or scripting, then convert edited rows back to PDB when you're done — pair with VCF_TO_CSV when you're relating a structure back to the variant that affects it.

Frequently Asked Questions

How does it read the fixed-width columns correctly?

It follows the official PDB specification's exact character positions for each field, rather than guessing from whitespace.

Can I convert edited CSV data back into a PDB file?

Yes, it serializes rows back into properly padded, spec-compliant PDB lines.

Built for anyone who needs to sort, filter or script against protein coordinates without a structural biology toolkit installed.

Read the related guide →