Hi Yu - we regularly model BrdU in our DNA chains with the "replace residue" function in coot. Model a normal thymine in the required position and then centre on the thymine. Then select :
Extensions > Modelling > Replace Fragment and type BRU into the dialog box. (see 5.17.3 of http://biop.ox.ac.uk/coot/doc/coot/Mutation.html#Mutation ) It will also add a superfluous OP3 atom to the BRU phosphate atom upon residue replacement which you'll need to delete. Make sure the flanking nucleotides of DNA can already be regularised/refined with coot (a version dependent issue i think) otherwise it won't link the BRU properly. Alan On 23/10/2011 21:03, zhang yu wrote: > 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 > >
