Install avogadro by entering the following commands in the terminal:
sudo apt update sudo apt install avogadro
Molecular Graphics and Modelling System
Avogadro is a molecular graphics and modelling system targeted at molecules and biomolecules. It can visualize properties like molecular orbitals or electrostatic potentials and features an intuitive molecular builder. . 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 plugin architecture and Python scripting . File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as Gaussian, GAMESS and MOLPRO output.