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 […]

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 […]

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 […]