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

[Almudena Ponce Salvatierra]

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
view.

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
puckers.

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,

Almudena

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
Germany
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