Category Archives: HOW-TO

Advanced: Combine 3D-SNFG with a Trajectory Smoothing Window

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 […]

Advanced: Change the material of the 3D-SNFG shapes

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 […]

Advanced: Color monosaccharide atoms according to SNFG

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 […]

Advanced: Introduce New Residue Names

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 […]