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