I'm new to Modeller. I have a protein segment I'm trying to model that consists of 2 domains. This protein has 4 very similar domains; 2 have been resolved and the other 2 have not (the ones I want to model). I go through the motions of aligning the sequences and building the model; however, the 2 domains I modelled are basically entangled. Thus, my question is, how can I keep this from happening (such as specifying a straight link between the domains instead of the current one that loops back, if this is even plausible)? Any suggestions are greatly appreciated.