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.