App created by Dr. Jared-Adolf-Bryfogle (jadolfbr@gmail.com); Lab of Dr. William Schief (schief@scripps.edu), in collaboration with Dr. Sebastian Raemisch (raemisch@scripps.edu) and Dr. Jason W. Labonte (JWLabonte@JHU.edu); Lab of Dr. Jeff Gray (jgray@jhu.edu)
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
The app prints out information for each glycan tree, including rosetta numbering, pdb numbering, internal-glycan numbering, and the connections of every residue in the tree. It is very useful when dealing with more than one glycan tree, or when one needs to work with particular components of the glycan.
Example command-line:
glycan_clash_check.default.macosclangrelease -include_sugars \
-s pose_with_glycan.pdb NOTE: It will not echo any PDB files, and will print the information to the screen.
group: carbohydrates:GlycanInfo
Opt: -res_info
Type: StringVector
Desc: Only output info for a specific residue or
residues (or full glycan roots).
Either rosetta resnum or PDBNumChain
as in Rosetta Scripts (133A).
Ex: -res_info 133A 140B 150C