Software for visualization of 3D models of chemical structures with atomic orbitals A number of programs are available that let you build, visualize, and analyze 3D models of chemical structures (I use Chem3D/ChemBio3D). Current versions usually include various possibilities for the calculation and graphical representation of molecular orbitals.



However, the resulting images can be overloaded or unclear. Introductory explanations using such images might be overdoing it. Therefore, many textbooks on organic chemistry use simple chemical structure diagrams based on atomic orbitals.



In particular for didactic purposes, I am looking for an intermediate solution. I would like to build, optimize, and visualize a 3D model of a chemical structure and show a graphical representation of the original atomic orbitals in the 3D model. Unfortunately, this option doesn’t seem to be available in Chem3D/ChemBio3D. Does any software exist that lets you build a 3D model of a chemical structure and visualize atomic orbitals?
As porphyrin mentions in the comments, have a look at Jmol.



It indeed does the rendering as in your original version, but with the many options (see this mo command documentation) and particularly interactivity provided by the scripting, I think you may pedagogically achieve what you are looking for. Proteopedia is a nice website where the efficiently use Jmol's scripting feature for educational purposes (try the green links).