[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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