Hi Ronnie, you will need to create a dictionary of the link in Jligand or Acedrg (ccp4i2) if we talk about ccp4 programs, and provide this as a LIBIN input in Refmac5.
In coot you will need to delete ND2 atom of Asn residue (if your dictionary contains link Lys NZ - Asn CG) and in menu calculate/modellling/make link join NZ and CG atoms. Best wishes, Misha Isupov ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Ronnie Berntsson <ronnie.bernts...@umu.se> Sent: 16 March 2022 14:57 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] How to make an isopeptide bond? Dear all, I have a protein structure that has 4 isopeptide bonds (between Lys and Asn pairs). However, I can’t for the life of me figure out a way to model this in in Coot (or by editing the pdb file, or some other method) so that I can refine it properly. Googling it hasn’t really helped much either, so I was hoping that someone here might know of an (preferably easy) way to do this? Best wishes, Ronnie ---------- Ronnie Berntsson, PhD Member of the Young Academy of Sweden Chair of the Swedish Society for Biochemistry, Biophysics and Molecular biology Department of Medical Biochemistry and Biophysics, Umeå University 90187 Umeå, Sweden e-mail: ronnie.bernts...@umu.se<mailto:ronnie.bernts...@umu.se> phone: +46 90 7865235 web: https://www.biostruct.umu.se/principal-investigators/ronnie-berntsson/ ________________________________ 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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7CM.Isupov%40exeter.ac.uk%7Cd4ba1aaa159444246f0108da075dbf25%7C912a5d77fb984eeeaf321334d8f04a53%7C0%7C0%7C637830396461464700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=oALvaxlFoC2K%2FhN%2F2HxvRrgrvIEw0vpB88uJqjsZWDk%3D&reserved=0> ######################################################################## 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/
