[phenixbb] DNA restraints

Martin.Laurberg martin at biology.ucsc.edu
Wed Aug 6 10:00:52 PDT 2008


Hej Jens,
You could use the custom bond distance and bond angle definitions, and
write them by hand if there's only a few to make.

http://www.phenix-online.org/download/cci_apps/  (and click phenix.refine
doc)

refinement.geometry_restraints.edits {
  zn_selection = chain X and resname ZN and resid 200 and name ZN
  his117_selection = chain X and resname HIS and resid 117 and name NE2
  asp130_selection = chain X and resname ASP and resid 130 and name OD1
  bond {
    action = *add
    atom_selection_1 = $zn_selection
    atom_selection_2 = $his117_selection
    distance_ideal = 2.1
    sigma = 0.02
    slack = None
  }
}

Good luck,

/Martin

--
Martin Laurberg, PhD
Noller Laboratory
225 Sinsheimer Laboratories
University of California at Santa Cruz
CA-95064 Santa Cruz
USA

Tel +1 (831) 459 35 84
Fax +1 (831) 459 37 37


On Wed, 6 Aug 2008, jens j birktoft wrote:

> Hi,
>
> Is there a way to restrain selected hydrogen bonds between base pairs during
> the refinement of DNA structures ?
> CNS has something like DNA_RNA.def if I remember correctly and I am looking
> for something of that nature.
>
> Cheers
>
> Jens
>
>
>
> --
> Jens J. Birktoft - e-mail: jens.knold at gmail.com
> slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
> use 212-749-5057 for ALL phone calls
>



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