Dear modeller users,

I have the following problem:

I have to model a homo-dimer. There is no template of dimer (there are several templates that cover just some parts of the monomer and thus I do use multiple templates to get a descent model of the monomer).
I have an alignment file that looks something like this:






On the positive side I have a list of constraints, so I want to rely on the constraints when I model the dimer interface.

The problems is that since the templates for each of the monomers have the same coordinates (modelling each of the monomers of my dimer) i do obtain a model of my dimer with the 2 monomer chains basically inter-twisted (so there is no any kind of interface in between the chains because the chains are nested one in another).
Also i can’t understand why, but one of the chains has secondary structure while the other doesn’t. I hoped the constraints file will push and orient the chains in the right possible way but it doesn’t seem the case.

Please suggest me any ideas to overcome this problem.
Thanks in advance.
Expecting reply from you guys.