Hi All, I build a ligand that is partly RNA and Partly a protein chain. In between I have a special nucleotide with a N bound to C3' (instead of O3'). it is : CC-PPU-Ala-Phe-Val. I have links in the .pdb file and the PPU is a known ligand to COOT. My links connect the N3' of the PPU with the C of Ala. nevertheless, if I try to regularize or refine the Ala keeps moving away from the PPU. The other link I defined between the C and the PPU works fine. What am I missing here ? Do I need to specify anything else than the LINK? I attached the .pdb file of my ligand for you to be able to load into coot and try playing with it yourself.
I look forward for your help. Best, Anat.
