[phenixbb] Making GDP (non-polymer) into an RNA monomer

[William Scott]

I've done just that with GTP, so with minor changes, this should work:

  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
    }
  }


Francis E Reyes wrote:
> All
>
> I need to attach a 5' modification, a diphosphate guanosine to my RNA.
> I figure GDP (from the monomer library) has everything I need.
> However, what needs to be done to make a connection with the next
> nucleotide in the chain (in both phenix.refine and coot) ?
>
> Thanks
>
> FR
>
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
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>
>
>
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