env = environ()
aln = alignment(env)

mdl = model(env, file='1M9D', model_segment=('FIRST:C','LAST:C'))
aln.append_model(mdl, align_codes=('1M9DC'), atom_files='1M9D.pdb')

aln.append(file='AIRE.ali', align_codes='AIRE')
aln.align2d()
aln.write(file='AIRE-mult.ali', alignment_format='PIR')
aln.write(file='AIRE-mult.pap', alignment_format='PAP')