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[modeller_usage] Taking into account additional residues

Hi all,
my problem is the following:

I want to model a structure based on another one. Both are trimers. My sequence (corresponding to the "unknown" proteins) has additional residues at the beginning of each chain, and I have to force them to make an alpha-helix. The problem is that when I try to add the restraints using as template the original chains-including PDB file and separating chains in the .ali file, the residues numbering seems to start from the residue 1 of the template, and I can't impose anything on my sequence.
I've tried too to edit the template PDB file in order to delete the information about chains and to obtain a "normal" numbering, but in this case, obviously, Modeller is not able to separate the subunits and generates strange distortions to keep in contact the boundary residues.
Last possibility would be to model separately the chains and to reconstruct the trimer at the end, but the modeling changes the coordinates and I can not imagine how to reassemble the single results.
Any suggestion?

thanks in advance

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