On 5/22/25 8:52 AM, Fred Pontes via modeller_usage wrote: > How can I apply a restraint between template and model, in order to have > the same relative position between the helices?
I guess I don't fully understand your question, because restraints are always applied to the model, and are constructed using template information - so a restraint "between the template and model" doesn't really make sense (restraints use internal coordinates such as residue-residue distances so the relative orientation of model and template is irrelevant). If the relative orientation of the two helices is correct in the template, but it isn't in the model, then the first place to look would be the alignment.
Possibly for one reason or another you have few restraints between the two helices. In that case you could certainly try adding an absolute position restraint on the z coordinate of the CA of each helix terminal residue; see features.ZCoordinate at https://salilab.org/modeller/10.6/manual/node109.html
Ben Webb, Modeller Caretaker