The saved .pdb file is imported into Blender using the Atomic Blender plugin by Clemens Barth. If bond information is missing from the .pdb file, converting it into an .xyz file and then back into a .pdb file in Avogadro fixes the problem. By merging and deleting unnecessary objects (i.e., caps at the ends of bonds), the number of vertices in the 3D model is lowered such that a smaller file size is obtained.