molekel

MOLEKEL is an interactive, three-dimensional molecular graphics package, represents molecules as wire frame, stick, ball-and-stick and spacefill representations, measures atom-atom distances, angles and torsion angles, can superimpose molecules, calculates and displays isosurfaces of electron and spin densities as well as molecular orbitals from the output of various electronic structure calculation programs, uses texture mapping to color code any surface according to e.g. the molecular electrostatic potential, is able to clip any surface by a clipping plane and to render it transparent, can animate and display vibrational modes, can animate geometry optimizations and multiple coordinate PDB and XYZ files, can display the dipole moment of a molecule. (Summary from the program web page.)

The official web page: http://en.wikipedia.org/wiki/Molekel

Typical usage

$ module add molekel
$ molekel