Dear Cryo EM,
In general, if you bring the two atoms at approximatively the correct distance
and do a real space refinement or regularization, a bond should be generated.
However, there are caveats:
1. Do the nucleotides belong to the same chain? If they belong to different
chains, they will not get bonded.
2. Do the atoms have the correct names for standard nucleotides?
3. An erroneous TER card between the nucleotides may also behind your
problem.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Cryo EM
Gesendet: Dienstag, 9. August 2022 03:41
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Making bonds
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?
Regards
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