Phenix in the past, and I’m assuming still, does not recognize “link records”. You’ll likely need to generate the peptide in AceDRG, making sure to link the carboxy- and amino-termini, and include the cif during refinement.
This was the only way I was able to get Phenix to properly refine an inhibitor covalently linked to an active site Cys. Thus, the same procedure may be required for your circular peptide. Best, Nick Clark On Sun, Aug 14, 2022 at 1:06 AM Jiang Xu <foxj...@gmail.com> wrote: > Hi Joel, > Thank you for your reply. I just got time to refine the circular > peptide structure 1 month later. I use MR to solve the structure. I made > the link(Calculate-->Modeling-->Make Link) as the guy who replied to my > question suggested. The link generated is a dashed line but disappeared > after refinement with Phenix. It seemed that the program didn't consider > the link made in coot as a valid bond and intentionally avoided forming a > bond between the C atom and the N atom. I still don't know how to fix the > problem. > Thank you, > Best regards, > Jiang > Lin Chen Lab > University of Southern California > > P.S. > coot manually made link between the C and N terminal > [image: unnamed.jpg] > After refinement > [image: unnamed (1).jpg] > > > > On Wed, Jul 6, 2022 at 3:29 PM Joel Tyndall <joel.tynd...@otago.ac.nz> > wrote: > >> 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://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C7254b01c56844333414808da7db2c0ca%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637960504076930467%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GR4GEfTFeUVE6RD6MMx2mNYCtKlnE5iuXkAqngHUiJ8%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 > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C7254b01c56844333414808da7db2c0ca%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C637960504076930467%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GR4GEfTFeUVE6RD6MMx2mNYCtKlnE5iuXkAqngHUiJ8%3D&reserved=0> > -- Nicholas D. Clark PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ######################################################################## 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/
