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Modelling domains

I have a protein with two domainswhich i would like to model. I have 3
template structures. One template (T1) has both the domains but with not
good homology, which I would like to use for the orientation of the 2
domains. The 2 structures are of 2 individual domains with very high
homology. I have tried to model my protein using template 1 (T1)and use
the ".ini" file from it to further refine the 2 domains. Now is there a way
how can i put these 2 back. Any suggestions. Or is there a better
Satyan Sharma