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Lisa Wang wrote:
> hi all,
> I have one structure contains dsRNA with two phosphate group at 5'.. I
> named
> the first residue GDP and got a cif file by running phenix.elbow. Then I
> refine my structure by running phenix.refine my.pdb my.cif. But the fist
> and
> the second residue do not link with each other, that is no bond between
> O3*
> of the fist residue and P of the second residue.
> Please give me some idea. Thanks
>

You have to explicitly link them.  Something like the following:

  geometry_restraints.edits {
    bond {
      action = *add delete change
      atom_selection_1 = "chain A and resid 1 and name O3\\*"
      atom_selection_2 = "chain A and resid 2 and name P"
      symmetry_operation = None
      distance_ideal = 1.59
      sigma = 0.01
    }
    angle {
      action = *add delete change
      atom_selection_1 = "chain A and resid 1 and name C3\\*"
      atom_selection_2 = "chain A and resid 1 and name O3\\*"
      atom_selection_3 = "chain A and resid 2 and name P"
      angle_ideal = 120
      sigma = 1
    }
  }