Russell Green wrote: > 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.
This suggests that your alignment is not correct, as Modeller will build models that look like your alignment template(s), by construction. You can certainly add your own distance restraints between domains, but I suggest you revisit the alignment first.
Ben Webb, Modeller Caretaker