[phenixbb] link restraints for modified nucleotides in RNA

[Jeff Headd]

Hi Gerwald,

Have you looked at these specific restraints in the .geo file? This
file will tell you what the target value is for each angle and should
match the definition found in the your restraints file.  If they do
not match then there may be a bug that we need to work out.  If you'd
like I'd be happy to look at your restraints .cif file and .geo file
if you could send them to me directly.

Jeff

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
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