The script functions by: Identify residues that contain a 6-membered ring AND have atom names C1, C2, C3, C4, C5, and O5 Determine the geometric center of the ring for residues from Step 1 Identify the geometric center of the connecting residue by 1) determining the oxygen that is connected to C1 and is NOT […]
The internal averaging VMD applies to coordinates to achieve Trajectory Smoothing via the graphical Representations window is not currently accessible to the 3D-SNFG script; however, it is possible to prepare a version of the carbohydrate-containing trajectory with smoothing applied by using Trajectory Smooth within the Tk Console. This additional script produces a copy of the […]
Please let us know if you have any questions or comments about the 3D-SNFG program.
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 […]
Changing the materials of representations can dramatically affect images. The default material for 3D-SNFG is AOShiny; however, this can be easily adjusted with a function on the command line: draw material Opaque This command can either be input via the Tk Console, or the command line that opens with VMD. Note that the material can […]
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’), […]
As an added bonus, the user can now color any monosaccharide according to the SNFG scheme by simply choosing the ResName option for the Coloring Method. After the 3D-SNFG script has been initialized (by pressing ‘g’ or ‘i’), the colors for each residue recognized within the 3D-SNFG script are assigned internally, and may be applied […]
If a residue is not recognized by the 3D-SNFG program, consider manually adding it to the script. Open the downloaded file (vmd.rc, .vmdrc, or 3D-SNFG.tcl) using any text editor. The residue names are defined towards the beginning of the script. It starts with Glucose and ends with Psicose, so the easiest way to find the […]
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.
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 […]