Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me.
What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in "Jligand". 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run "Real-space refine" in coot The problem... "Real-space refine" fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
