Hi Peter - i've managed to do this for some nucleic acids by using a custom cif file that contained planar restraint links for each type of base pair, and then specifying a phenix .params file that applies these cif links to specific base pairs in my model. e.g. for a G-C base pair (DNA-RNA hybrid), the cif file would have... data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name GdCr Gd . . Cr . . GdCr data_link_GdCr loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd GdCr p 1 N1 0.02 GdCr p 1 C2 0.02 GdCr p 1 N2 0.02 GdCr p 2 O2 0.02 GdCr p 2 C2 0.02 GdCr p 2 N3 0.02 GdCr p 1 N1 0.02 GdCr p 1 C6 0.02 GdCr p 1 O6 0.02 GdCr p 2 N4 0.02 GdCr p 2 C4 0.02 GdCr p 2 N3 0.02 ...and in the .params file... refinement.pdb_interpretation.apply_cif_link { data_link = GdCr residue_selection_1 = chain T and resname Gd and resid 23 residue_selection_2 = chain P and resname Cr and resid 7 } I also had to combine it with h-bond base pair restraints with the usual refinement.geometry.restraints.edits settings. Alan On 19/04/2010 12:23, Peter Grey wrote:
Dear all,
I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ?
I am grateful for your advice,
Peter
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