To the point of refining in Phenix, once you have the glycans in place it should be automatic except for the first link of the tree. Send me the model and I can provide the necessary files for refinement.
Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Fri, Jul 14, 2023 at 2:03 AM Keitaro Yamashita < kyamash...@mrc-lmb.cam.ac.uk> wrote: > In the monomer library, pyr-SER and pyr-THR links are defined for the > O-glycosylation. A monomer should belong to the "pyranose" group in > the library (or in a user-provided dictionary). > > Best regards, > Keitaro > > On Fri, 14 Jul 2023 at 09:22, Jon Agirre > <000017a7df66b7b3-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > 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 < > 00008d0668c7d48d-dmarc-requ...@jiscmail.ac.uk> 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 > >> Fax: +44 1158468002 > >> email:jonas.ems...@nottingham.ac.uk > >> > http://www.nottingham.ac.uk/research/groups/structural-biology/index.aspx > >> > >> 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 > > > > > > ######################################################################## > > 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/ > ######################################################################## 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/
