[phenixbb] How to define link in phenix (rna3p) ?

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Thu Apr 7 09:40:17 PDT 2011

> 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.

You can use the apply_cif_link parameters.

> 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.

The _chem_comp.group value is ignored by phenix.refine.
The classifications are obtained via analysis of the atom names
and the bonding in the monomer definitions.

>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}

It is strange that it thinks there is a peptide but still applies two
rna/dna links. Could you send me (not the list) the part from the pdb
file with the Q1 chain?


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