Input format: pdb-atom
Uses Bio.PDB to determine the (partial) protein sequence as it appears in the structure based on the atom coordinate section of the file (requires NumPy).
Output format: fasta
This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a '>' line. Resulting sequences have a generic alphabet by default.
How to convert from pdb-atom to fasta ?
You can also convert between these formats by using command line tools.
On Windows install WSL, on
Mac
or Linux start
terminal
Install BioPython
Run following script:
Or you can use this site as online pdb-atom to fasta converter by selecting your formats &
file.
Sequence Converter Home page
from Bio import SeqIO
records = SeqIO.parse("THIS_IS_YOUR_INPUT_FILE.pdb-atom", "pdb-atom")
count = SeqIO.write(records, "THIS_IS_YOUR_OUTPUT_FILE.fasta", "fasta")
print("Converted %i records" % count)