Avogadro, edit and visualize molecules with this open source program

about avogadro

In the next article we are going to take a look at Avogadro. This is a free, open source, molecular editing application for Gnu / Linux, Windows and MacOS. It is a program that can be used in computational chemistry, molecular modeling, bioinformatics, materials science, and many other fields.

The application is used in VTK for analysis and visualization capabilities. It also supports volume representation for point data or flow lines for vector fields. It offers flexible, high-quality rendering and a powerful plug-in architecture. Is about a simple and easy-to-use software, ready to be used by students and researchers. Avogadro is free software that you can redistribute and / or modify under the terms of the GNU General Public License, published by the Free Software Foundation, either version 2 of the License or any later version.

Unlike other web-based 2D / 3D molecular viewers, Avogadro uses OpenGL directly and offers native desktop packages. This application uses a set of standards that allow computer programs to use 2D / 3D hardware rendering functions (GPU). Avogadro supports out-of-the-box multi-threaded computation and processing, has interactive tools, commands, and custom Python scripts.

General characteristics of Avogadro

sulfuric acid molecule

  • It’s a multiplatform program, so we can use it in Gnu / Linux, Windows and Mac OSX.
  • Is about a light program offering high performance.
  • Despite all that it offers, it has some minimum hardware requirements.
  • The program is translated into different languages, as they are; Chinese, French, German, Italian, Russian, Spanish, and some others.
  • Its interface is clear and easy to use.
  • Includes a large set of tools for measurement, alignment, visualization, manipulation and drawing.
  • It will also offer us extensions bundled with the extensions manager.
  • Will allow us import from various applications.
  • Supports many open formats.

periodic table

  • We will be able consult the periodic table.
  • We will can build 2D and 3D molecule models.
  • Allows you to insert, build and modify predesigned modules (DNA, RNA, Fragment, SMILES, Peptide, Polymer).
  • Visualization of electrostatic potential maps.
  • Use of analysis of atoms in molecules (Bader): QTAIM and WFN.
  • Molecule-surface interactions.

forming molecules

  • We will can manipulate, measure and align with tools. We can also count on selection, auto-rotate, and auto-optimize tools.
  • The team of Avogadro offers all users a set of tutorials so developers can help, compile from source and contribute your extensions. They also publish clear API documentation.

Install Avogadro on Ubuntu

Avogadro is available as a flatpak pack for Ubuntu system. Before installing this program, we must have this technology enabled in our system. If you don’t already have it and you use Ubuntu 20.04, you can follow the guide that a colleague wrote on this blog a while ago.

When you already have this technology enabled on your system, you can proceed with the installation. You just need to open a terminal (Ctrl + Alt + T) and run the following command in it to install Avogadro:

install avogadro

flatpak install flathub org.openchemistry.Avogadro2

After the installation, you can run the program looking for the pitcher on our team. You can also open the Avogadro molecular editor using the following command in the terminal:

avogadro pitcher

flatpak run org.openchemistry.Avogadro2


In order to remove this program, we will only need to open a terminal (Ctrl + Alt + T) and execute the command in it:

uninstall avogadro

flatpak uninstall org.openchemistry.Avogadro2

Avogadro is an advanced molecule viewer and editor, which is designed for cross-platform use in fields such as computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. What’s more offers flexible quality rendering with a powerful plugin architecture.

This software is an open source project, which aims to be used worldwide without restrictions by all developers, researchers and students who want to. It can get more information about this program at project website or from your page on GitHub.

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