Convert PDB structure (observed residues) to FASTA

Provided by bugaco.com

Extract the protein residues present in a PDB structure's atom coordinates as FASTA.

PDB structure (observed residues) → FASTA

  • This reads residues present in the structure's coordinates; missing residues will not appear.

Maximum file size: 50 MB. The file is checked before conversion.

About this conversion

The converter reads records in the input format and writes them in the output format. Data that the output format cannot store may be lost. The form above explains the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. If your output needs a sequence type, provide the matching molecule type.

from Bio import SeqIO

count = SeqIO.convert("input.pdb-atom", "pdb-atom",
                      "output.fasta", "fasta")
print("Converted %i records" % count)

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