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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb