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.
