I'm not sure it will help and frankly, I don't have any better idea, but here is how one can change the weight of secondary structure restraints.
Before starting, I would check the .geo file to make sure the model deviates quite significantly from the target in the restraints you are going to adjust. This will also give an idea what to adjust.
First parameter to play with is secondary_structure.nucleic_acid.scale_bonds_sigma. Default is 1. All sigmas for h-bond length will be multiplied by this number. The smaller number is tighter restraints.
Next, I would switch parallelity restraints for basepares to planarity. This should make them really planar. This can be achieved by nucleic_acid.base_pair.restrain_planarity=True, nucleic_acid.base_pair.restrain_parallelity=False parameters for individual basepairs. They can be changed in the GUI for individual base pairs in the selection editor, see screenshot below.
If you prefer command-line, or working with parameter file, you can run
phenix.secondary_structure_restraints model.pdb file.param
with file.param containing for example (changing parallelity to planarity):
secondary_structure {
enabled = True
nucleic_acid {
base_pair {
restrain_planarity = True
restrain_parallelity = True
planarity_sigma = 0.2
}
}
planarity_sigma = 0.2
}
}
This will produce a parameter file describing SS restraints which can be edited further. For example, you can define planarity_sigma.
For the sake of completeness, the parameters are listed here: https://phenix-online.org/documentation/reference/secondary_structure.html
Hope it will help,
Best regards,
Oleg Sobolev.
}
}