On 27/05/2023 00:43, Nicholas Clark wrote:
I have a cysteine residue that is oxidized and needs to be modeled as
CSO. In the past, when "replace residue" was used to substitute for
CSO, the CSO would "behave" during real-space refinement and
essentially take the place of the Cys. However, when Cys is replaced
by CSO now the CSO is behaving as an "external ligand" and does not
maintain covalent bonds to the residue before or after (repulsion
between CSO & preceding and subsequent residue). The only way I can
get it to maintain covalent bonds in Coot is to add CSO as a monomer
and place it before merging into the chain and renumbering the residue
(afterwards, real space refinement behaves the same as direct
replacement of CYS->CSO). Similarly, during refinement with Refmac,
only one of the CSO conformations will maintain its position, the
alternate conformation breaks the linkage to the preceding residue.
*TLDR: CSO replacement of CYS not working in Coot or Refmac, acting as
external ligand*.
As you may know the monomer library has been undergoing substantial
reworking over the last several months. Is the group of the CSO in your
dictionary "peptide"?
Paul.
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