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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AboutPDB to CSV

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

Reviewing atomic coordinates in a spreadsheetFeeding structure data into custom analysis scripts

The PDB to CSV tool is compatible with:Structural Biology ToolsPyMOLRCSB PDB. This tool alone can help you manage and analyze your data effectively. However, a composed workflow using VCF TO CSV, BED TO CSV may provide even more powerful data processing capabilities. Consider exploring these related tools for a comprehensive data solution.
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.

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.

Developed by HowToCSV for our valued CSV Haters worldwide.