hello there I am in the process of refining a protein structure complexed to DNA promoter site. I ran into difficulty as i try to move a few bases into patch of electron density that is obviously meant for them. dragging the bases with real space refine zone and/or regularize zone neither break open the phosphate back bone bounds or turn everything into knots. I know there is nothing wrong with the naming convention of my bases since I changed them from DT to Td after similar blog. Any suggestion on this matter would be greatly appreciated.
Norm