You will need to add the "link" line to the PDB file so the software recognises the covalent bond.
See the pdb file for 6U6K Hope this helps J From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Jiang Xu Sent: Thursday, 7 July 2022 10:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] circular peptide structure refinement Hello everyone, I have a peptide that forms a peptide bond between the N terminal and C terminal. I used X-ray crystallography to solve the structure and found the N and C terminals are pretty close to each other with extra electron densities clearly showing that they form a peptide bond. However in Coot I could not make the peptide bond, the two terminals seem to repel each other when I do real space refinement in coot and, couldn't form the peptide bond. Any suggestions on how to do it? Thank you, Best, Jiang Xu Lin Chen Research Group Molecular and Computational Biology Department of Biological Sciences University of Southern California ________________________________ 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://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8e27251437384d075b9808da5f9d22ca%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637927427557539545%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xUCZ%2BQsYKRSrHmAM%2F0qDFoK2p1T%2BwalD1GErObuAwWU%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/
