I am trying to generate .pdb files from fasta sequences using BioPython SeqIO module to parse them to Pymol, and fab command:
from Bio import SeqIO for seq_record in SeqIO.parse(file, "fasta"): pymol.cmd.do("fab %s, %s" % (seq_record.seq, seq_record.id)) pymol.cmd.save("%s.pdb" % seq_record.id, "all")
The script produces the files without displaying any errors, but they are either empty or the sequence is incomplete.
Does someone already encounter this problem? Is something wrong with my script?
Note: the exact same happens if I include a handle for the SeqIO module.