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 […]

If multiple PDB files are loaded within VMD, the representation will only be drawn on the ‘top’ molecule. In order to apply the representations to any of the other files, change the ‘top’ molecule by double clicking the blank space in the T column in the Main Window. Alternatively, change the top molecule via the […]

The easiest solution is to change the residue name in the PDB file to one that is already recognized by the script. Use any text editor to open the PDB file and modify the fourth column. Find and replace is useful, or use a substitution method via the command line (i.e. ‘sed‘ or ‘vi‘). If […]

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 […]

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 […]