[modeller_usage] alignment for multiple chain modelling

Hello,

For multichain modelling (ex. for a hetrodimer), Is it possible to force the alignment program in modeller to choose particular chain for the alignment?. For example use only template A chain for 1st chain in the sequence and template B chain for 2nd chain in the sequence.

env = environ() aln = alignment(env) mdl = model(env, file=3gsn, model_segment=("FIRST:A, "LAST:B)) aln.append(file='seq.ali', align_codes='seq') aln.align2d() aln.write(file=align.ali, alignment_format='PIR')

Thanks for any leads.. Sal