Hello, I have a DNA substrate in which only a few of the backbone phosphate linkages have been replaced with a phosphorothioate analog.� Currently, I can make a .cif file for the bases that have the replacement, but after running refinement in REFMAC5, the bases are not connected to the rest of the DNA strand.� I have tried adding "CONECT" lines to the pdb file to force connection, but is didn't work.� I have tried to make .cif files for each strand in PHENIX, but this fails also.�
This is the only thing keeping me from being done with this structure.� Any advice or suggestions would be great. ~Beth
