For reference, I am using the 3.8 Version of PyRosetta.
After using the glycosylate_pose() function, I can see sites on my pose (a protein read in through pose_from_pdb). However, the sugars at these sites appear to have a lot of clashing with other parts of the protein. I wanted to use a function like glycan_sampler() which supposedly uses glycan_relax_mover. I can’t seem to find documentation though, and when I use help(glycan_sampler), it is asking for inputs that I don’t think I can provide (e.g. I don’t know why there is a ResidueSelector as input in the function). I could also be reading it incorrectly. If you could please post an example of how to “relax the glycans,” I’d appreciate it a lot! Thanks.
Working with Glycans: https://new.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans
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