Hi. I came across with the following post when I was dealing with a similar issue (adding a modified nucleotide to RNA). I could create .cif using elbow/reel as well, but I was wondering where to define the link type between residues in phenix.

For RNA, I typically see "rna3p', but with my newly created residue linked to normal oligo, the link is formed, but recognized as Link ID 'p'. Also, the newly created molecule is recognized as 'peptide', although I defined _chem_comp.group in .cif file as RNA.

------------------------------------------
Chain: "Q1"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 74
          Classifications: {'RNA': 2, 'peptide': 1}
          Modifications used: {'5*END': 1, 'rna3p': 2}
          Link IDs: {'p': 1, 'rna3p': 1}
------------------------------------------

Any input will be appreciated.

Sincerely,

"T"

On Wed, Nov 17, 2010 at 7:43 AM, Gerwald Jogl <Gerwald_Jogl at brown.edu> wrote:
> Hi All,
>
> I am refining several modified nucleotides in ribosomal RNA
> (N2-methyl-guanosine and similar). While the restraints generation with
> phenix.reel work quite well, I am unable to get the phosphate oxygen
> restraints applied properly. Phenix.refine recognizes the links but for some
> reason the phosphate groups come out quite distorted...
>
> For example, angles after refinement:
> O3 (1) - P (2, modified) - OP2 (2) = 80 deg and
> O3 (1) - P (2, modified) - OP1 (2) = 127 deg
>
>
> Here is part of the phenix.refine log on reading the coordinates:
>
>    Chain: "A"
>      Number of atoms: 32526
>      Number of conformers: 1
>      Conformer: ""
>        Number of residues, atoms: 1513, 32526
>          Unusual residues: {'MA6%rna3p': 2, '5MC%rna3p': 3, '5MC%rna2p': 1,
> '7M
> G%rna3p': 1, '2MG%rna3p': 1, 'UR3%rna2p': 1, 'M2G%rna3p': 1, '4OC%rna3p': 1}
>          Classifications: {'undetermined': 11, 'RNA': 1502}
>          Modifications used: {'5*END': 1, 'rna3p': 1318, 'rna2p': 195}
>          Link IDs: {'rna3p': 1318, 'rna2p': 194}
>          Chain breaks: 1
>
> I am at a loss about how to fix this as all links and restraints seem to be
> in place.
>
> Many thanks for advice,
> Gerwald