[phenixbb] Modified DNA residue
pafonine at lbl.gov
Wed Jan 11 14:22:49 PST 2017
we need to have a closer look to understand what's happening...
Could you please send us these PDB file:
- original (before modifications);
- file after modifications;
- file after refinement;
- cif file.
On 1/11/17 14:15, Melissa Ford wrote:
> I'm having working on modeling a sulfur on the phosphate backbone of
> DNA in replace of one of the oxygens and have encountered some
> restraint problems. I've successfully managed to replace the oxygen
> with a sulfur in the proper geometry in a pdb, generate a cif file for
> the modified residue (adenosine 5'-phosphorothioate), and run an
> initial refinement. Upon that refinement, a few errors occur. First,
> since the phosphate bound to the sulfur is the first atom of the
> modified residue the angle between the O3' (of the neighboring
> residue) - P- S is not recognized and forced into an unfavorable
> geometry. When trying to add that additional angle to the cif file, I
> get an error. Aditionally, the change causes Phenix to not recognize
> the chirality of the C3' that the phosphate is bonded to and forces
> the ribose into a planar conformation. I am sure there is something I
> am missing that allows phenix to recognize this new residue as a
> modified nucleotide so that it knows these restraints. Any insight on
> this would be great. Thank you!
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