This writes out the residue sequence of the chain to an alignment file.
file specifies the name of the output file. atom_file and align_code specify the name of the chain's associated atom file, and its alignment code, respectively; suitable values can be obtained from chain.atom_file_and_code(). comment, if given, specifies a comment to prepend to the alignment file.
format specifies the format of the output file; see alignment.write(). PIR or FASTA formats are supported.
chop_nonstd_termini trims non-standard terminal residues in exactly the same way as for chain.filter().Example: See chain.filter() command.