[phenixbb] DNA double helix through crystal symmetry
osobolev at lbl.gov
Sat Mar 25 08:32:12 PDT 2017
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:
excessive_bond_distance_limit = 10
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.
On Fri, Mar 24, 2017 at 8:08 PM, Oleg Sobolev <osobolev at lbl.gov> 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 <wtempel at gmail.com> wrote:
>> how could one restrain DNA base pairing across a crystallographic axis?
>> Are secondary_structure.nucleic_acid restraints "symmetry-aware"?
>> Thank you.
>> Wolfram Tempel
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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