Category Archives: FAQ

FAQ: How were the sizes of the 3D-SNFG shapes selected?

The diameter of the sphere in the 3D-SNFG representation is exactly 4 Å, and the other shapes are scaled around the sphere. This size for the sphere was chosen based on the cross-section of a monosaccharide ring, which is approximately 4 Å in one direction and 6 Å in another. Although we tested shapes at […]

FAQ: What does “ERROR) No molecules loaded” mean?

This error message is harmless. The provided vmdrc files apply specific representations to the first molecule that is loaded into the program (i.e. proteins displayed in NewCartoon and hetero atoms as licorice). If a molecule is not loaded upon initializing VMD, either by double-clicking the PDB file or through the command line (i.e. ‘vmd 3SGJ.pdb’), […]

FAQ: Are structures available to test my setup?

Yes, the structures that were used to generate each of the Glycan images in the Gallery may be downloaded by clicking on the name of the respective structure. Additionally, each PDB referenced in the gallery is available directly from the RCSB database.

FAQ: Does the code discriminate between D- and L- residues?

Symbols within the SNFG nomenclature refer to either the D or L form of the monosaccharide based upon what is most common in nature. The 3D-SNFG code does NOT differentiate between L and D residues. For example, the red triangle within the SNFG refers to an L-Fucose; however, both L and D Fucose are represented […]

FAQ: How are modifications represented (i.e. sulfate and phosphate)?

Sugar modifications are not currently displayed in 3D-SNFG, although the base shape is shown. The SNFG icons are an effective method for communicating the modifications on residues. For example, the following is a heparan sulfate fragment built with the GLYCAM Webtool: Using the 3D-SNFG icons conveys both the residue name and sulfation position. Representing the […]

FAQ: Why are some of the shapes missing?

Check the PDB file to ensure that the ring atoms are properly named. For most monosaccharides, they should be C1, C2, C3, C4, C5. If the residue is a sialic acid, the ring atoms should be C2, C3, C4, C5, C6, and O6. Example error message from command line: ERROR) vecsub: two vectors don’t have […]

FAQ: Why are all of the shapes missing?

First, try using a file that has already been tested, such as this file generated from the GLYCAM Web-Builder OR PDB ID: 3SGJ. If those files work properly, but your original does not, check the file to ensure the pdb is in the proper format (compared to the provided files). For example, a .pdbqt file […]