[phenixbb] How to include restrains to DNA as A-DNA or B-DNA

Oleg Sobolev osobolev at lbl.gov
Tue Feb 23 10:04:13 PST 2016

Dear Zhe,

Presently, there is no option to enforce the particular sugar pucker in
DNA. Nevertheless, Phenix still applies restraints to sugar rings so they
would stay in a particular conformation based on input geometry. So the way
to go is make desired conformation for your sugars in e.g. Coot and Phenix
should keep them in it. If it is not the case for you, we will need more
information to investigate further.

Regarding to secondary structure restraints for nucleic acids, presently
they enforce planarity of base-pairs, correct hydrogen bonds in base pair
and parallelity of stacked bases.

Best regards,
Oleg Sobolev.

On Mon, Feb 22, 2016 at 7:50 PM, Zhe Li <lizhelizhelizhe at hotmail.com> wrote:

> I am refining a protein-dsDNA complex structures at 2.4-3 A. Based on the
> phosphate distance, I can predict if particular nucleotide is A DNA
> (C3’-endo) or B DNA (C2’-endo). I want to add restrain to to the specific
> nucleotides as A or B DNA. But secondary_structure_restraints for nucleic
> acid does not seem to have options for this. Any suggestions?
> Thanks
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