Thanks, I appreciate all the help from you guys. A brief summary,
As Sabine, Paul and Ed pointed, change the "_chem_comp.group" in "data_comp_list" to DNA is the key for coot to recognize it. As Alan said, "Extension>Modeling>Replace Residues" could also insert BRU into DNA chain without any modification of cif file. 在 2011年10月24日 上午3:52，Alan Cheung <[email protected]>写道： > Whoops, i meant > > Extensions> Modelling> Replace Residue > > and not replace fragment. > > > > > On 24/10/2011 09:43, Alan Cheung wrote: > > 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 > >> > >> > -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
