[modeller_usage] Re: restraint distance between template and model

[Modeller Caretaker <>]

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
-- 
             https://salilab.org/modeller/
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