Yes - this area is a mess.
However I got round it to some extent by naming the nucleotide as a
standard one ((in your case C) , then adding the heavy atom, and creating
the LINK records between that C and the additional atom(s).
Probably at deposition the moiety should be renames as 5CM but that
Dear experts,
I am trying to insert a non-natural nucleotide (5CM, methylated cytosine) at
6th position in a 13-mer DNA. I have generated the CIF file for 5CM using ELBOW
(Phenix). I tried replacing the Cytosine with 5CM and linking the O3' of -1
nucleotide with P of 5CM and o3' of 5CM with P
