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')