Hi Jon, Thanks for the reply. They’re going in as HETATMs. I didn’t try changing them to ATOMs because I checked my previous structure’s PDB file (one that worked fine) and they were in it as HETATMs.
I have changed them to ATOMs and it’s still “misbehaving” in real space refinement but shows a “link line” to the preceding and subsequent residue. But that appears to be due the linkage lines I previously entered into the header, as removing them removed this behavior. I put the file with the CSO as ATOMs through Refmac refinement and the same behavior occurs, loss of one conformation’s covalent bond to the preceding residue. They are changed back to HETATOMs by Refmac. Best, Nick Clark On Fri, May 26, 2023 at 8:14 PM Jon Cooper <jon.b.coo...@protonmail.com> wrote: > Hello, is the CSO going into the PDB file as ATOM'S or HETATM's? > > Best wishes, Jon Cooper. jon.b.coo...@protonmail.com > > Sent from Proton Mail mobile > > > > -------- Original Message -------- > On 27 May 2023, 00:43, Nicholas Clark < ndcla...@buffalo.edu> 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 > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7C51caf8b31a1f421b080508db5e473e64%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638207432431196718%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=h0p6OIAPiXNP2fWRzyNFBZnFnuiVgcv3tTzFJt9oKFc%3D&reserved=0> > > -- 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/
