Hello, is the CSO going into the PDB file as ATOM'S or HETATM's? Best wishes, Jon Cooper. [email protected]
Sent from Proton Mail mobile -------- Original Message -------- On 27 May 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. > > 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 ######################################################################## 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/
