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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 gets rpound the refinement glitch..

Eleanor



On Thu, 2 May 2019 at 06:13, Abhishek Suman <[log in to unmask]> wrote:
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 of +1 nucleotide in coot using "Make link". This adds a "LINK" line in the pdb file. But, upon refinement in Phenix, the LINK information goes off.

Can anyone please help me with the covalent linking of 5CM with -1 and +1 nucleotides? Also, the saved PDB file doesn't contain the CONECT line for the HETATM. I want to know, how can I append the CONECT information in my PDB for 5CM?

Thanks in advance

Regards
Abhishek

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