I had this issue before and tried several ways to fix it. The best way that works for me is to edit the PDB and cif files of this unnatural amino acid for Coot or Phenix. The goal is to allow COOT and Phenix to recognize it as an 'amino acid', not a random HETATM, so they can add peptide bonds and apply appropriate geometry restrictions in the real-space refinement automatically. But I will be interested to learn better ways if there are any.
Here is how I do it: 1. Make a PDB file with Phenix's elbow based on the
chemical structure of this amino acid. I usually use MDL or SDL files. 2.
Change the names of atoms in the PDB file. You have to name the main chain
atoms of amino acids specifically so COOT can read them as 'amino acids'.
Open a PDB file of any protein and you will see those specific names (C, O,
N, C, CA, CB). 3. Use this PDB file to make a cif file. In the cif file,
you have to define this amino acid as an 'L-peptide' or 'D-peptide' in the
ligand type line. I attached a cif file of L-cysteine. Pay attention to the
ligand definition (' L-peptide') and the names of atoms. 4. Open the PDB
and cif files in Coot. Merge this amino acid into your structure and change
its numbering. Now you should be able to do real space refinement on it as
if it is a natural amino acid.
Also, there are already many unnatural amino acids in COOT or Phenix
database. You just have to find the right 3-letter codes.
Hope it helps.
Cheng
On Mon, Jun 14, 2021 at 10:05 AM Hall, Gareth A.F. (Dr.) <
gh...@leicester.ac.uk> wrote:
> Dear ccp4bb,
>
>
>
> I am having an issue with a non-standard amino acid in Coot. I have a
> cyclic peptide that is stapled using two cysteine residues and a methylene
> bridge. I have prepared a restraints file using ACEDRG for a methyl
> cysteine as a surrogate for one of the cysteine residues and I have fitted
> it into the density in the appropriate space within the peptide where the
> cysteine would have been. I have made LINKs between the appropriate atoms
> of the previous and subsequent amino acids in the peptide chain to the
> methyl cysteine, as well as between the methyl component of the methyl
> cysteine and the bonded cysteine residue to form a methylene bridge. The
> resulting pdb file runs without fault within REFMAC, but when I open the
> refined files in Coot and try to triple refine the methyl cysteine within
> the peptide chain Coot pushes all the residues away from each other.
>
>
>
> Please can someone advise as to what I am missing/doing wrong!
>
>
>
> Many thanks in advance,
>
>
>
> Gareth
>
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--
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Cheng Zhang
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CYS.cif
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