FAQ: How do I draw 3D-CFG objects on a molecule other than the most recently added one?

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 command line (i.e. ‘mol top 1’).