Thank you, Paul. Indeed, I’ve forgotten to change the subject. Apologies for misleading.
Vaheh From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Paul Emsley Sent: Monday, March 24, 2025 3:21 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Pyroglutamic acid On 21/03/2025 21:06, Oganesyan, Vaheh wrote: -- Hello, Hello Vaheh. The N-terminal Gln in one of the structures cyclizes on itself forming pyroglutamic acid. Coot has one as a ligand under name PCA. The CCP4 monomer library, yes. However, even after removing OXT the geometry of the amino acid and its fit to density could be better. OK, but what treatment did you give your PCA to get it into such a state? Is there an option use it as an amino acid like seeing it in “Mutate & Auto Fit” place and not as a ligand? PCA in the monomer library is a non-polymer. Coot won't allow you to add non-polymers to a protein chain. It is not a ligand at the end. In that case, change the group to peptide in the dictionary. I don't recall if Coot deletes the OXT for you in "Mutate & Auto Fit" - but it should be trivial to do post-hoc. Sorry for posting in CCP4 bb and not Coot bb. That's not a problem. However, the fact that you replied to a message in the "Words to avoid" is - it means that your question and this answer (for whatever it's worth) will be buried in the wrong thread. A new topic should have a new thread. Paul. ________________________________ 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://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. ######################################################################## 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/
