The PyMOlyze open-source project has been renamed QMForge, and it continues to help you analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.

The unrelated PyMOL open-source project may be of help with 3D visualization of proteins, small molecules, experimental electron density, molecular surfaces, and molecular dynamics trajectories.