Victoria Ann McKenna wrote: > If I was trying to restrain the secondary structure of the > target but in some instances this differs from the > secondary structure of the template, how would MODELLER > restrain, or over ride the restraints of the target (i.e. > how does it choose which restraints to use and when?).

Modeller always uses all restraints, so there is no choice to be made here. If you are worried about user-supplied restraints conflicting with the default homology-derived restraints, you can weaken or remove the latter.

Ben Webb, Modeller Caretaker