Hello Prof. Bonvin
I updated my PDB file and my glycoprotein nomenclature is also fine. But I still getting “XXX” in place of NAG and BMA glycosylation when I uploaded my PDB in HADDOC2.4 server. Please help me to resolve this issue.
Thank You
Also I am not able to see any glycosylation residues when I visualized the structure using visualize residue option.
Same story - there are just visual tools.
Check the resulting docked models. If displaying in line mode, you should see it.
But for proper visualisation rather download the models and use e.g. PyMol