Privateer for UCSF ChimeraX: Carbohydrate structure validation and visualization

Modeling 3D carbohydrate structures, either as ligands or covalently bonded to proteins, still presents a number of challenges. As such, carbohydrate structure validation is a key step in the modeling process. The Privateer software package has long provided methods to aid in this validation, considering unlikely ring conformations of the sugars, stereochemistry, comparison to known glycans, and unlikely linkage torsions. However, uptake of these tools depends on the pipeline used for structure solution. It is therefore important to make glycan validation available in as many model building programs as possible. To this end, we have created a Privateer bundle for ChimeraX. This bundle provides intuitive access to key validation metrics for carbohydrates present in a structure model within the molecular visualization program while working on your structure solution, as well as providing the ability to visualize monosaccharides in the structure using 3D glycan symbols to aid in understanding of interactions. The Privateer bundle for ChimeraX can be installed from ChimeraX's toolshed: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxprivateer.