Alignment of PDB template with non-continuous sequences of target protein

Hi,
I would like to model the following situation. Having two globular domains, A and B, whose PDB's are available. I 'm building new proteins consisting on domain B inserted in the middle of A (adding some linker), leading to a chimera protein A1-B-A2. I know that the domains keep their own structure to a high extent because they both maintain their properties.

So I would like to know whether it is possible at all to assign spacial coordinates through my PDB template to non continuous regions of my target protein. This would be like splitting in two the PDB template.

I tried all possible combinations (providing one template or the other, with or without the alignment, providing or not distance restrains for A1 + A2 or B, etc, and none of the worked so far)

Thanks a lot in advance!