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.
########################################################################
To unsubscribe from the COOT list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1
This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
