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How to relax glycans after glycosylating sites on a pose?

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How to relax glycans after glycosylating sites on a pose?

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

Post Situation: 
Mon, 2021-03-22 09:44

The glycan sampling algorithms, both GlycanSampler and GlycanTreeModeler, have not been published yet, which is why they do not have documentation.  The GlycanTreeModeler has current best-settings and can be used by passing a residue selector. I'm hoping to get a biorxiv up in the next few weeks with the work.



Mon, 2021-03-22 09:56

Thank you, Jared!

Mon, 2021-03-22 17:05