Convert PDB structure (observed residues) to PHYLIP alignment (interleaved)

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Convert a PDB structure (observed residues) sequence file to PHYLIP alignment (interleaved).

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

PDB structure (observed residues) → PHYLIP alignment (interleaved)

  • This reads residues present in the structure's coordinates; missing residues will not appear.
  • PHYLIP keeps only the first 10 characters of each record ID (and replaces : and ; with |). IDs that become identical are rejected.
  • The selected output is an alignment format. Every sequence must be the same length and already aligned. This does not create an alignment.

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 notes under the Convert file button list the important limits for this pair.

Run it with Biopython

For batch work, you can use Biopython's SeqIO.convert function. This pair needs no molecule type argument.

from Bio import SeqIO

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

Sample input file: PDB structure (observed residues)

Copy this example into a file, or download it, to try a PDB structure (observed residues) conversion.

Download sample (sample.pdb, 15.0 KB)

Samples are small illustrative files. Some come from the Biopython test suite (see the project's sample notes); they are not real study data.

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