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.
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