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Hi Yu, A few things which caused this happened to me with other non-standart nucleotides: - the hydrogen of the 3'O of the BrdU is defined as 3'OH in the cif file - order of the atoms in the pdb file ie compare the position of the 3'OH with the standard dNTP in the PDB - is the 3BrdU defined as 'DNA' in the cif file? (under 'data_comp_list') Maybe that helps! Sabine On 10/23/2011 09:03 PM, zhang yu wrote: > Hi, > > My DNA chain has a internal modification of 5-Bromo-2กไ-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 > >