I'm trying to model a flexible protein where two highly rigid domains move in respect to each other, and would like to model some of the states between the two extremes in the templates. When I model with the open and closed form of the protein as templates, I only get open and closed forms af the target. As I initially understood the spatial restraints, they are an average of the restraints extracted from the templates. But it seems to me now, that when theres a spatial restraint of f.ex 6� from one template and 8� from the other, modeller tries to match either 6� or 8� in the target, where 7� is not OK. Please correct me if I misunderstood. Is it possible to change this behaivor to a flat bottom potential? To take the former example: So that any distance in the range 6-8� is equal, and the potiential then rising outside that? Due to glibc compat. errors i've used mod6v2 and not the newest 8v0.
Best Regards Esben Jannik Bjerrum
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