<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-family: calibri, arial, helvetica, sans-serif; font-size: medium;" class="">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! </span></body></html>