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Authors: Dr. Jared Adolf-Bryfogle (jadolfbr@gmail.com), Dr. Jason Labonte (JWLabonte@jhu.edu), and Dr. Sebastian Rämisch (raemisch@scripps.edu)

PIs: Dr. William Schief (schief@scripps.edu) and Dr. Jeffrey Gray (jgray@jhu.edu)

Reference

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000; https://doi.org/10.1101/2021.09.27.462000

Autogenerated Tag Syntax Documentation:

---

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) A ResidueSelector for carbohydrates and individual carbohydrate trees. Selects all Glycan residues if no option is given or the branch going out from the root residue. Selecting from root residues allows you to choose the whole glycan branch or only tips, etc.

<Glycan name="(&string;)" branch="(&string;)" branches="(&string;)"
        ref_pose_name="(&string;)" include_root="(false &bool;)" />

• branch: Set the residue to select from. These can be the branch points of the glycans or carbohydrate residues from which to select the downstream branch from. Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out. Pose (23) or PDB numbering (24A)
• branches: Set the residues to select from. Separated by spaces or commas. These can be the branch points of the glycans or carbohydrate residues from which to select the downstream branch from. Like the rest of a tree from a particular position. That position could be the trunk or individual branches, which keep branching out. Pose (23) or PDB numbering (24A)
• ref_pose_name: If using a Reference Pose, set the name
• include_root: Should we include the root (branch/branches) residues in our selection or just go from that?

---

See Also

• WorkingWithGlycans

RosettaCarbohydrate Apps and Components

• Movers

  • GlycanTreeModeler - The optimal way to model glycan trees. Uses GlycanRelax internally.
  • SimpleGlycosylateMover - Glycosylate poses with glycan trees such as man5, man9, or other complex trees.
    
  • GlycanSampler - Component used in GlycanTreeRelax to do the torsional and side-chain sampling.

• Residue Selectors

  • GlycanResidueSelector - Select specific residues of each glycan tree of interest.
  • GlycanLayerSelector - Select glycan layers
  • RandomGlycanFoliageSelector - Randomly select a set of glycan residues

• Applications

  • GlycanInfo - Get information on all glycan trees within a pose
  • GlycanClashCheck - Obtain data on model clashes with and between glycans, or between glycans and other protein chains.

• Other

  • Application Documentation: List of Rosetta applications
  • Running Rosetta with options: Instructions for running Rosetta executables.
  • Comparing structures: Essay on comparing structures
  • Analyzing Results: Tips for analyzing results generated using Rosetta
  • Solving a Biological Problem: Guide to approaching biological problems using Rosetta
  • Commands collection: A list of example command lines for running Rosetta executable files