[phenixbb] Modified DNA residue

Pavel Afonine pafonine at lbl.gov
Wed Jan 11 14:22:49 PST 2017

Hi Melissa,

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! 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170111/696189b4/attachment.htm>

More information about the phenixbb mailing list