Dear Vaheh, In Coot 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 On Mon, 24 Mar 2025 at 07:20, Paul Emsley <[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 > -- Oliver Smart ######################################################################## 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/
