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 >> >>
