Re: [phenixbb] DNA double helix through crystal symmetry

25 Mar 2017

      Hi Wolfram,

It turned out that secondary structure restraints are not symmetry-aware.
I'm sorry for my previous misleading response.
In example of 9dna you pointed out, one can manually set custom bonds that
can go across symmetry by adding the following to parameter file:

geometry_restraints.edits {
  excessive_bond_distance_limit = 10
  bond {
    action = *add delete change
    atom_selection_1 = resid 1 and name N1
    atom_selection_2 = resid 8 and name N3
    symmetry_operation = y,x,-z+1
    distance_ideal = 2.9
    sigma = 0.1
    slack = None
  }
}

Also note that standard base-pair hbond restraints also include angle.
There is currently no way to set angle restraints across symmetry.

I'll edit documentation accordingly.

Best regards,
Oleg Sobolev.

On Fri, Mar 24, 2017 at 8:08 PM, Oleg Sobolev  wrote:
...
Hi Wolfram,
I believe that secondary structure restraints are "symmetry-aware", so
just try to use them. If they don't work for you, let me know.
Best regards,
Oleg Sobolev.
On Fri, Mar 24, 2017 at 9:52 AM, wtempel  wrote:
...
Hello,
how could one restrain DNA base pairing across a crystallographic axis?
Are secondary_structure.nucleic_acid restraints "symmetry-aware"?
Thank you.
Wolfram Tempel
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