the easiest way is to build the corresponding alignment, that reflects all the template-target sequence equivalences along the whole complex.
For a two-chain situation you can check FAQ 4 on page 107 in the manual.
best wishes, Andras
Dr Nicolas Le Novere wrote: > > Dear modellers, > > My template is a homooligomer. I would like to model similar oligomers > either with N times the same sequence, or with different homologous > sequences. What is the best format for the alignment and/or top > > (How to force MODELLER to model the sequence X on the chain A and the > sequence Y on the chaine B?) > > Regards, > > -- > Dr Nicolas Le Novère http://www-alt.pasteur.fr/~lenov > Dpt of Zoology, Univ of Cambridge, Downing street, Cambridge CB2 3EJ, UK > tel: +44 1223 336623 fax: +44 1223 336676 e-mail: email@example.com