Now I'm thinking of cutting out these helices and manually position them approximately where I want them. But I fear that this will case headache at the "joint".
This is very likely. If the distance would be too big, there will be no connection. If you will specify links manually, for long distances this may cause instability in "joint" region during refinement.
Is it possible to use the manual positions as a reference for positional restraints,
No. Unfortunately, the reference_coordinate_restraints are not designed to take other model.
Or is there a better way of refining this structure?
Maybe you can try "Real space refine zone" in Coot and drag the piece of model into the density there maintaining the reasonable geometry during the process?
Best regards,
Oleg Sobolev.
Regards,
Daniel
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