Dear All, Thank you for all replies. Yes, I discovered "Replace Residue" option with help of @Aibara, Shintaro<mailto:[email protected]> and Oliver Smart. (Why Replace and Mutate exist separately? Would be great to know.) However, the CCP4 library contains PCA.cif where it is mentioned as "P-peptide" (depending on version of CCP4 it also mentioned as "Non-polymer"). Misha Isupov was very instrumental to mention this because without reading in the new library file for PCA with "L-peptide" to Coot "Real Space Refine" was throwing PCA and neighboring amino acids out of density. However, I haven't refined the model yet in Refmac, but hoping the PCA will be correctly recognized.
Vaheh From: Oliver Smart <[email protected]> Sent: Monday, March 24, 2025 8:52 AM To: Oganesyan, Vaheh <[email protected]> Cc: [email protected]; Paul Emsley <[email protected]> Subject: Re: [ccp4bb] Pyroglutamic acid Dear Vaheh, In Coot 0.9.8.95<http://0.9.8.95> (ccp4), if you want to mutate to a non-standard amino acid, then instead of using the "Mutate & Auto Fit", you need to use the "Edit" -> "Replace Residue" option and type in the 3-letter code. Before doing this, load a restraint dictionary with _chem_comp.group set to "L-PEPTIDE," as Paul suggests. The Grade2 restraint dictionary for PCA already gets the group correct, but you can edit the CCP4 library dictionary. Once the mutation has occurred, use the "Real Space Refine Zone" and select the N-terminal residue and the following residue to fix the peptide bond geometry. This works great for me. Hope this helps Oliver PS The coot documentation has a section on this: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Mutating-to-a-Non_002dStandard-Residue<https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/web/docs/coot.html#Mutating-to-a-Non_002dStandard-Residue> On Mon, 24 Mar 2025 at 07:20, Paul Emsley <[email protected]<mailto:[email protected]>> wrote: 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> -- Oliver Smart ________________________________ 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/
