Because of non-standard atom names, group names of some monomers were changed to NON-POLYMER. In this case the hydrogen atom is only the problem, so changing group to peptide works unless you have hydrogen. Moreover, in CSO, the problematic hydrogen is removed when forming a peptide link. The details are described in the paper Paul mentioned.
Refmac would work, if "refmacat" (explained in the paper) is used. The command is already available in the latest CCP4 update, but not from the interfaces at the moment. Best regards, Keitaro On Sat, 27 May 2023 at 04:02, Nicholas Clark <ndcla...@buffalo.edu> wrote: > > Hi Paul, > > Thank you for providing that information. Editing the restraints for CSO > corrected the issue! Your assistance is greatly appreciated. I figured I was > missing something :) > > Best, > > Nick Clark > > On Fri, May 26, 2023 at 10:55 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> > wrote: >> >> >> On 27/05/2023 03:46, Nicholas Clark wrote: >> >> Paul, >> >> Yes, it appears that the upper level group is "NON-POLYMER". However, there >> is an alias at the bottom that does state polymer. >> >> >> Hi Nick, >> >> >> In Coot: Edit -> Restraints... -> CSO -> OK -> Change "Non-POLYMER" to >> "peptide" and press enter in the entry, then "Apply" >> >> Now you can refine your CSO in Coot. >> >> Paul. >> >> >> >> Best, >> >> Nick Clark >> >> >> On Fri, May 26, 2023 at 10:37 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> >> wrote: >>> >>> >>> On 27/05/2023 03:23, Nicholas Clark wrote: >>> >>> 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. >>> >>> >>> Due to other priorities, Coot is not up to speed with the developments of >>> my colleagues: >>> >>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10167671/ (Section 2) >>> >>> What is the value of _chem_comp.group ? That is (for the moment) what Coot >>> cares about. >>> >>> >>> 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 > > > > -- > 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 ######################################################################## 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/
