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 <[email protected]> Im Auftrag von Cryo EM Gesendet: Dienstag, 9. August 2022 03:41 An: [email protected] 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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
