Hi Matthew, I would recommend against creating a composite component (amino acid + sugar), in favour of modelling the covalent linkage explicitly. In general, the recommended approach is to use an AceDRG link dictionary. See here for practical options, recommendations and discussion: https://journals.iucr.org/d/issues/2021/06/00/ir5021/ir5021.pdf
However, if you're dealing with residues very commonly involved in glycosylation then it could be that the covalent linkage will be detected and an appropriate AceDRG dictionary used by default when refining with REFMAC5/Refmacat. To check whether that is the case, see here (Table 6, and Table 5): https://journals.iucr.org/d/issues/2021/06/00/ir5022/ir5022.pdf Best regards, Rob Dr Rob Nicholls Principal Computation Scientist Scientific Computing Department Science and Technology Facilities Council Research Complex at Harwell Rutherford Appleton Laboratory Didcot, OX11 0QX On 13 Nov 2024, at 11:35, Matthew Snee <matthew.sne...@manchester.ac.uk> wrote: Hi All This is a related question to one I saw earlier. I would like to add an O-linked glycan, If my map was very high resolution I would be tempted to simply use ligand restraints and add a link record, but the data is lower resolution so the bond-length and angle will Not be sensible without refinement with proper restraints, and I probably need geometry restraints to help narrow the fitting possibilities down and make a good judgement of the conformation. My default solution is to generate the full amino acid with the sugar in AceDRG and then rename the necessary atoms and header to turn it into a residue that COOT will recognise as a non-standard amino acid. Is this the "correct" way with respect to what the PDB expects these days? Best wishes Matthew. Matthew Snee, PhD Post-doctoral Research Associate The Baldock Lab | Michael Smith Building C3.214 | Wellcome Trust Centre for Cell-Matrix Research |Division of Cell Matrix Biology & Regenerative Medicine| School of Biological Sciences| Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT Lab Tel: +44 (0)161 306 2869 <Outlook-r2puf3nd.png><Outlook-cell-matri.png> ________________________________ 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/
