Openbabel: Generate 3D depiction?
Open Babel does not generate "ball and stick 3D depictions" directly, because it's not a molecular visualization program.

That's why we started Avogadro.

There are a few formats supported in Open Babel to write out 3D depictions, e.g.:


POV-Ray
STL - for 3D printing
Point Cloud - outlining the Van der Waals surface


But you can make a pseudo-3D "ball and stick" depiction in the SVG format:



obabel [file] -O file.svg -xS