XYZ PDB
File conversion

Convert XYZ to PDB

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Is it possible to convert XYZ to PDB?
Yes - XYZ converts to PDB.

Convert to Protein Data Bank format for biomolecular tools/viewers. Open Babel ('obabel in.xyz -O out.pdb') or Avogadro export. Note PDB adds residue/atom-naming that XYZ lacks.

Also to PDB: MOL · CAR · LIT

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Tested on macOS, Windows & Linux
Last verified Oct 2026

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How to convert XYZ to PDB

Converting a .XYZ file to .PDB lets you open the content in software that prefers the .PDB format, though some details may change compared with the original. We are still putting together the list of programs that handle .XYZ files.

A full step-by-step guide for this conversion is on the way; the information above is drawn straight from our database.

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