To the best of my knowledge, there is no o-glycan equivalent of the Coot glyco plugin. We (as in YSBL, York) are working with others to provide tools to build all kinds of glycans, but there's nothing you can use at this point. I would deal with it like I'd do with other modifications, get monomer, make the link, repeat. Links are likely to be part of the CCP4 monomer library already. Also, they are likely to be short-ish glycans, so hopefully the task won't be too onerous. One issue depending on the resolution is the identification of the monosaccharides. But you can have a look at some of the many possibilities here: https://www.cell.com/cell/pdf/S0092-8674(18)30053-9.pdf?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867418300539%3Fshowall%3Dtrue It might help to look at other o-glycosylated structures in the PDB. You can now do pretty powerful searches on the PDB. Alternatively, I'm sure someone in my team could provide a list of all o-glycans Privateer can detect in the PDB. Hope this helps, Jon
On Fri, 14 Jul 2023 at 09:03, Jonas Emsley < [email protected]> wrote: > Dear All > > > > We have a crystal structure with O-glycans for the first time attached to > a Ser and a Thr sidechain > > > > If anyone can recommend the procedure for adding these in coot and > refining them in phenix /refmac that would be greatly appreciated > > > > All the best > > > > jonas > > > > > > > > ################################## > Dr Jonas Emsley > Professor of Macromolecular Crystallography, > Nottingham Biodiscovery Institute > School of Pharmacy, > University of Nottingham, > University Park, > Nottingham. > NG72RD > Tel: +44 1158467092 <+441158467092> > Fax: +44 1158468002 <+441158468002> > email:[email protected] > http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx > > *https://orcid.org/0000-0002-8949-8030 > <https://orcid.org/0000-0002-8949-8030>* > > > > > > > > > > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please contact the sender and delete the email and > attachment. > > Any views or opinions expressed by the author of this email do not > necessarily reflect the views of the University of Nottingham. Email > communications with the University of Nottingham may be monitored > where permitted by law. > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK ######################################################################## 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/
