[phenixbb] hydrogen-bond restraints for Watson-Crick base pairs

Nathaniel Echols nechols at lbl.gov
Tue Jun 22 14:37:47 PDT 2010

On Tue, Jun 22, 2010 at 2:21 PM, Scott Classen <sclassen at lbl.gov> wrote:

> 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

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.)

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