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-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
>
>
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