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 […]
Carbohydrates in the PDB and VMD For reasons that are mostly historical, carbohydrates are currently not treated well in non-specialist databases such as the PDB or in visualization software such as VMD. Efforts are underway to improve the situation. In the meantime, this exercise will explain some of the problems, and offer some ways to […]
These instructions apply to residues from GLYCAM06-h and later. They also require that you use pre-existing residues in the GLYCAM prep file database. However, there are brief notes regarding modifications of existing residues, if that is required. The method for adding derivatives to GLYCAM residues is very similar to the method for building branched structures. […]