Hi Sabine, Thanks for your suggestions.
I checked the cif file of BrdU. the hydrogen of the 3'O of the BrdU is defined as HO3' in BrdU cif file, in stead of 3'OH. The standard dNTP cifs define it as HO3' too. In PDB, there is no atoms for hydrogen, as I excluded them. The BrdU is defined as "UBP" as I named in my cif file (under 'data_comp_list') Any suggestion? I attached my cif and pdb of BrdU, could you take a look at it? Do you have any suggestion of program generating cif for non-standard nucleotides? Thanks Yu 在 2011年10月23日 下午3:50，Sabine Schneider <sabine.schnei...@mytum.de>写道： > 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-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
UBP.pdb
Description: Protein Databank data
UBP.cif
Description: CIF chemical test
