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 <[email protected]> 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 <[email protected]> > 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/ >> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC10167671%2F&data=05%7C01%7Cndclark2%40g-mail.buffalo.edu%7Cb0d84cd36871481df00308db5e5dcb42%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638207529177153336%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=e5MD%2Bzb8EazA%2FPWRxJ%2FRf5JSvFmGl%2Bgv2n92c%2FEL6%2BI%3D&reserved=0> >> (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 > <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%7Cb0d84cd36871481df00308db5e5dcb42%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638207529177153336%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=pUzaBQe3y4y4yEQZgMM94qxclCaOck7QP6q8HWrabEE%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/
