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*. I've tried adding a "Link" definition to the header for both conformations but this does not fix it. Any suggestions on how to resolve this issue? Best regards, Nick Clark -- 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 ######################################################################## 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/
