Dhirendra K Simanshu wrote:
> Hi everyone,
>
> I am trying to refine a structure which contains acetolysine (acetyl
> group attached to Lysine residue) in one of the polypeptide. I have
> refined acetolysine present in peptide using Refmac after adding the
> link information in the ligand cif file. After refinement it has
> linked acetolysine properly to polypeptide and seems to have refined
> it quite well. I was trying to do real space refinement for this
> stretch of peptide which contains acetplysine in coot. I have read the
> linked cif file using read monomer library option in coot. However,
> during real space refinement it breaks the link and refines it as an
> indiviual ligand not linked to aother amino acids as it should have
> been. I was wondering how I can refine the acetolysine in coot using
> "real space refinement" without breaking it from the polypeptide.
I suspect that your dictionary for acetyl lysine is not complete or
correct. Did you check the _chem_comp group?
Paul.
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