Dear all: I tried to build 5’-Br-dU in my coordinate. I imported Br-dU from monomer lib (coot) and put it in the position, merged the molecules, renamed the Chain ID and renumber the residues, everything was ok. However, when I did refinement with Phenix (using elbow to generate cif file for Br-dU) afterward, in the resulting PDB, the Br-dU were always found disconnected with the adjacent nucleotide. In coot, I could manually fix this problem with real-space refinement, but it seems that the Phenix always fall to do that. In addition, when using real-space refinement for nucleotide in coot, the hydrogen always falls apart. Is there anyone encounter the similar problems or know how to deal with them? Many thanks! Cui sheng
