You May try "Builder" panel embedded in Pymol to make covalent bond. Best Fulvio
Inviato da Outlook per Android<https://aka.ms/AAb9ysg> ________________________________ Da: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> per conto di Hsuan-Ai <hsuan-ai.c...@uni-wuerzburg.de> Inviato: lunedì, agosto 28, 2023 6:54:01 PM A: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Oggetto: [ccp4bb] How to make covalent bond for modified nucleic acid Greeting to all, I am struggling to place modified nucleotides into an oligonucleotide strand. I built the ligand restraint dictionaries both in Acedrg or Elbow; the generated liogands look fine, but the covalent bond between the ligand and the modification site cannot be generated, also in vain when following the Acedrg tutorial (where additional covalent bond restraint was generated). I also tried to edit the pdb file directly by specifying which atom links to which. It, nevertheless, did mot work as I imagined. How do you usually make ligand link to protein / nucleic acid via covalent bond? Is there some trick to tell the program the existence of covalent bonds? Any suggestions are heartily appreciated. Thank you in advanced! Best regards, Ai ######################################################################## 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## 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/
