env = environ()
aln = alignment(env)
mdl = model(env, file='1H8C')
aln.append_model(mdl, align_codes='1H8C', atom_files='1H8C.pdb')
aln.append(file='1D3Z.seq', align_codes='1D3Z')
aln.align2d()
aln.write(file='1D3Z-1H8C.ali', alignment_format='PIR')
aln.write(file='1D3Z-1H8C.pap', alignment_format='PAP')