Whether you are a chemical engineer, student, teacher, or just a chemistry enthusiast, visualizing atoms, molecules, and chemical compounds can be very difficult. It becomes even more frustrating when you have to illustrate it for other people. Fortunately, there are apps out there that can visualize these elements for you. Avogadro is one such app. Avogadro is a free and open-source molecule editor where users can input chemical compounds and elements and construct a visual image for them.
Avogadro is available for the three main operating systems; Windows, Mac, and Linux. There are no minimum recommended specs for Avogadro, so there should be no problem when trying to run it regardless of the operating system you are using. Of course, using advanced hardware and OS would help it perform more smoothly.
Avogadro has a simple interface that is composed only of a toolbar, preview window, and options panel. The toolbar contains the editing tools you will need to create 3D graphics of molecules. Additional options for each tool will be displayed at the options panel on the left side of the app window. Finally, the 3D graphic can be viewed in the preview window opposite of the options panel.
Avogadro's editing tools are very intuitive and easy to use. There are nine main tools for creating the 3D molecule models: Draw, Navigate, Bond-centric Manipulate, Manipulate, Selection, Auto-rotate, Auto-optimize, Measure, and Align.
The Draw Tool is used to draw and adjust molecules in the 3D model while the Navigate Tool lets users view the model by panning, rotating, and scaling across the window. The Bond-centric Manipulate Tool allows users to adjust the bonds and angles between molecules while the Manipulate Tool adjusts the molecules themselves. Additionally, the Selection Tool can be used to select specific parts of the model. Auto-rotate and Auto-optimize let users set the model to rotate continuously and optimize molecular geometry, respectively. Finally, the Align Tool repositions the molecule according to a certain axis while the Measure Tool measures bond lengths and other dimensions.
As an open-source software, the source code of Avogadro is completely available online which can be modified and edited by interested contributors. Avogadro can also be improved by adding extensions and plug-ins. The app can also support a large selection of file formats including CML, XYZ, SDF, Mol2, and more.
For the Chemists and the Wannabes
Being able to visualize molecules has a lot of uses for anybody in the chemistry industry. With that in mind, Avogadro is a must-have for people interested in chemistry. It will help both students and teachers to improve learning skills as well as professionals who just need a 3D model of visual aid for molecules. So be it elements, simple compounds, or complex bonds, Avogadro is definitely capable of rendering 3D models for you.