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[modeller_usage] How to introduce a covalent bond in a model?

I want to link N-end of the chain alpha with C-end of the chain beta in
my peptide. Terminal acids are quite near to each other (4 A), thus it
is possible. 
I have made up some workarounds like switching the chains in pdb and seq
files before making the alignment for modeller etc.; I dont like it
I suggest that there should be some universal function built-in modeller
for this kind of purpose. Do you know how to manage this?

Thank you. I appreciate your help.