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

Almudena Ponce Salvatierra maps.farma at gmail.com
Tue Feb 23 00:34:26 PST 2016

Dear Zhe,

I think Phenix can handle it without the need of specifying whether it will
be A or B. These might be too "strong" constrains in a way from my point of

Your DNA may be mostly B if it is unmodified, with the exception of some
part of the helix that has some C3´-endo puckers and therefore there "it
would be A", say. By default the nucleic acids restraints are on, I would
just keep working and refining, safest way to go indeed is to place the
phosphates where they should be, Phenix will take care of assigning the

If you want to compare your dsDNA with an ideal A type of helix DNA or B
type of helix DNA, you can just build yourself some withing coot. You find
this option under calculate/other modelling tools/ideal RNA/DNA.

I hope this helps,

Best wishes,


2016-02-23 4:50 GMT+01:00 Zhe Li <lizhelizhelizhe at hotmail.com>:

> 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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Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
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