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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
