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multiple domains

I have the following question:
I wish to model a series of homologous proteins (28 in total) for
which I have the structure of the first and the 26th in order of
sequence homology (ranging from ca. 55% to ca. 20%). The protein is
made of two domains. The two available structures are quite similar
except for the orientation of one domain with respect to the other
(significantly off). What is the best approach to model sequences #2
to #25 and #27-#28??? Is there an accepted protocol in order to model
multidomain proteins? I know that one of the biggest problems with
modelling protein structures is encountered when you have more than
one domain, that is, to model relative domain orientation. Is there a
way out? How would you proceed using Modeller???