Hey Paul, I found the dictionary entry for CSO, it appears to be in the "peptide" group (under CCP4-8.0->lib->data->monomers->c->CSO.cif):
"loop_ _chem_comp_alias.comp_id _chem_comp_alias.group _chem_comp_alias.atom_id _chem_comp_alias.atom_id_standard CSO *peptide* HN2 H2" I've attached the file I have for your reference, as I may not be looking in the correct place. Also, if I'm looking in the wrong file location, please let me know. Best, Nick Clark On Fri, May 26, 2023 at 10:04 PM Nicholas Clark <ndcla...@buffalo.edu> wrote: > 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 <pems...@mrc-lmb.cam.ac.uk> > 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 > -- 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/
CSO.cif
Description: Binary data
