Free online PDB to TXT converter

A program, editor, or archival workflow may require a readable .txt file instead of a .pdb file. The correct conversion method depends on whether the PDB contains molecular records, Palm OS database records, or an e-book.

What the PDB format is

.pdb is an ambiguous extension used by several unrelated formats:

• Protein Data Bank files are text files containing atomic coordinates, residues, models, and other molecular records. Researchers, molecular visualization applications, chemistry programs, and molecular-dynamics software use them.
• Palm Database files contain records and metadata for Palm OS applications. They are usually binary and may use application-specific structures or compression.
• PalmDOC, zTXT, and other e-book PDB variants store book content in formats designed for legacy Palm readers. Their internal structures differ from both scientific PDB files and ordinary Palm databases.

Identify the source before converting. Renaming file.pdb to file.txt changes only the extension; it does not decode binary records, decompress content, or correct character encoding.

What the TXT format is

.txt is a container-free plain-text format that stores characters and line breaks without application-specific formatting. It opens in Notepad, code editors, scripts, spreadsheet programs, and version-control tools.

TXT can contain the original text of a molecular PDB file, extracted e-book text, or a newly generated table of records. It does not inherently preserve molecular bonds, fixed database indexes, images, hyperlinks, bookmarks, compression, metadata, or document formatting. Export as UTF-8 when the source contains non-ASCII characters, but use the source application's encoding information when converting legacy Palm data.

How to convert a scientific PDB file

Most Protein Data Bank files are already plain text. If you need an identical text copy, duplicate the file and change the extension:

cp structure.pdb structure.txt

On Windows Command Prompt, use:

copy structure.pdb structure.txt

This preserves the original bytes but is technically a file copy, not a structural export. You can also open the file in a code editor and use File → Save As; avoid word processors because reflowing lines can damage the fixed-width columns used by PDB records.

For a reformatted export:

1. Open the file in PyMOL, UCSF ChimeraX, VMD, or another molecular application.
2. Choose the program's File → Export or Save As command.
3. Choose a text-based PDB export when the destination expects standard PDB records, or export a delimited atom table when it expects columns.
4. Save as .txt and check that atom names, residue names, coordinates, and model records remain intact.

A table can also be generated with Biopython, but it is not a faithful PDB copy:

from Bio.PDB import PDBParser

structure = PDBParser(QUIET=True).get_structure("model", "structure.pdb")
with open("atoms.txt", "w", encoding="utf-8") as output:
    for atom in structure.get_atoms():
        residue = atom.get_parent()
        x, y, z = atom.get_coord()
        output.write(f"{residue.get_resname()}\t{atom.get_name()}\t{x:.3f}\t{y:.3f}\t{z:.3f}\n")

Install the dependency with pip install biopython. The resulting tab-separated file contains selected atom data and omits other PDB records unless the script writes them explicitly.

How to convert a Palm or e-book PDB file

For PalmDOC and compatible e-book files, use an application that supports the specific subtype. Calibre can import many legacy Palm e-book files: add the book, choose Convert books, select TXT as the output format, and inspect the result for missing chapters, page breaks, and character errors. Support is not universal because PDB is only a container family name, not one e-book specification.

For a Palm application database, export from the original Palm application or a compatible synchronization utility. Use Export, Save As, or a delimited format such as CSV when available, then save the exported text as .txt. A text editor or generic file-copy command cannot normally decode binary database records.

You can also convert a supported PDB file on 101convert.com for free without installing software. Confirm the detected PDB subtype before conversion and avoid uploading confidential records, personal data, or unpublished research.

Quality and compatibility limits

Scientific PDB files use defined column positions, so line wrapping, automatic whitespace changes, or spreadsheet editing can corrupt coordinates and record alignment. Keep the original .pdb file and treat the TXT file as a working copy.

Palm and e-book conversions may remove compression, images, hyperlinks, bookmarks, record IDs, database metadata, and proprietary fields. Replacement characters such as � indicate an encoding problem; exporting again with UTF-8 helps only when the source application decodes the original bytes correctly. Changing the extension cannot recover text that was already misdecoded.