Hello friendly Phenix developers,
According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:
"hydrogen-bond restraints for Watson-Crick base pairs"
How do I use this? I couldn't find any documentation... or is it automagic?
Automagic, I hope. Start with "main.secondary_structure_restraints=True", and it will attempt to find existing base pairs by analyzing hydrogen bonds. If your geometry is still a little screwy, the parameter syntax is like this:
refinement.secondary_structure.nucleic_acids {
base_pair {
base1 = chain "A" and resseq 1
base2 = chain "B" and resseq 10
}
}
One piece of advice: make sure your structure has either all hydrogen atoms where they should be, or none at all - if you're missing any, the secondary structure restraints will probably break. The automatic mechanism will also restrain protein helices and sheets, but you can easily turn this off (restrain_helices=False restrain_sheets=False). It will probably be necessary to fiddle with the sigma and slack parameters for hydrogen bonds; it isn't clear yet how much these need to be tuned for individual structures, but the defaults don't always work best for all structures.
I am working on a brief sort-of-article on the secondary structure restraints, which has more information about the general mechanism (currently more focused on proteins, which is perhaps a defect). I'll send you a copy of the current draft. (A modified version of this will eventually become the official documentation.)