On 09/08/2022 02:40, Cryo EM wrote:
Hi everyone,

In one my PDBs, I see that there is a linkage break in ribonucleotides. Specifically one of the phospodiester bond seems to be broken and thus O3' needs to be bonded to P atom of next nucleotide. What is the easiest way to do this in coot ? Or any other software? I tried "make link" option in coot but it seems it just created link in PDB and not bond?


A link should not be needed if one nucleotide comes immediately after the other one in the same chain.

It might be that they are so far apart to begin with that Coot doesn't consider them bonded. Use Ctrl arrow-keys to move the O3' to within 3A of the P and give a quick sphere refine to test.

Paul.

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