Hi Wolfram,
It turned out that secondary structure restraints are not symmetry-aware. I'm sorry for my previous misleading response.
In example of 9dna you pointed out, one can manually set custom bonds that can go across symmetry by adding the following to parameter file:
geometry_restraints.edits {
excessive_bond_distance_limit = 10
bond {
action = *add delete change
atom_selection_1 = resid 1 and name N1
atom_selection_2 = resid 8 and name N3
symmetry_operation = y,x,-z+1
distance_ideal = 2.9
sigma = 0.1
slack = None
}
}
Also note that standard base-pair hbond restraints also include angle. There is currently no way to set angle restraints across symmetry.
I'll edit documentation accordingly.
Best regards,
Oleg Sobolev.