I'm building a model of a voltage-sensitive ion channel using Kv1.2/2.1 paddle chimera structure as a template (pdb: 2r9r). Although voltage-sensing (S1-S4) and pore (S5-S6) domains of the template come as a single chain, I get in the model more or less arbitrarily oriented VS and pore domains: the angle between them varies from ~0 to ~180 degrees [for two slightly different alignments]. For Kv, this angle is ~45 deg.
I was thinking that for a single-template modelling this should not be the case, since both domains are defined explicitly in the same coordinate system. This only might be treated normal when two different templates are used, and there's no additional restraints to stick them together.
Does anyone knows what's my problem? Do I misunderstand something?