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: [email protected] slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 use 212-749-5057 for ALL phone calls