Molecular Graphics and Modelling System - Avogadro

Avogadro is a molecular graphics and modelling system targeted at molecules and bio-molecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder.

Avogadro Features include:
 * Molecular modeller with automatic force-field based geometry optimization
 * Molecular Mechanics including constraints and conformer searches
 * Visualization of molecular orbitals and general isosurfaces
 * Visualization of vibrations and plotting of vibrational spectra
 * Support for crystallographic unit cells
 * Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry packages
 * Flexible plug-in architecture and Python scripting

Avogadro Installation:
Open the terminal and type following command:

sudo apt-get install avogadro

After successful installation you can open Avogadro from Unity 'Dash' or from the GNOME menu (Application > Science > Avogadro)

When you open Avogadro without loading a file it defaults to using the Draw Tool. This tool is the main one that will be used when drawing a new molecule. The screen shot below shows Avogadro on GNOME. The tool dock is located in the top of the left hand of the interface denoted by the pencil icon.

Check the Avogadro docs for more details - here or check out Youtube for tons of videos on building all different kinds of molecules using Avagadro.