Hey Paul, I'm not sure how to check that? Would you be able to provide a resource to check this?
Best, Nick Clark On Fri, May 26, 2023 at 9:21 PM Paul Emsley <[email protected]> wrote: > > 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. > > > -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
