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
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
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, ExtensionModelingReplace Residues could also insert BRU
into DNA chain without any
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
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 Sabine said, you need to make sure that the monomer is defined as DNA
type. The best way to figure out how to do this is to look at the
standard monomer library for nucleotide, e.g.
$CCP4_LIB/data/monomers/d/DA.cif.
On Sun, 2011-10-23 at 18:44 -0400, zhang yu wrote:
Hi Sabine,
Thanks for
