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://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/
