Hello Wei,
is the modified base defined as DNA in the cif? (see below)
Is the O3* or O3'? You need the latter.
And check whether there are three hydrogens on the O3. You need to
either remove one from the cif file manually, or name them according to
a normal DNA base. (In the latter case, by making the phosphodiester
bond, one should be removed, if coot/refmac/phenix know that this is DNA...)
Hope that helps!
Sabine
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
GdX G 'Guanosine ' DNA
35 23 .
#
On 15/07/14 11:14, Wang, Wei wrote:
Hi,
There is a problem about modified DNA refinement.
I generated one CIF file of a modified DNA base using eLBOW software
of PHENIX. However I found the modified DNA could not be linked to the
downstream DNA when I refined it in the COOT. Then I generated another
CIF file using sketcher of CCP4, but the problem still existed.
Is there any expert to help me?
Thanks!!
Best
Wei
