Four 3D molecular visualizers compared

The Nature Trail


Modern chemistry and biochemistry are hard to understand without 3D models. In this article, we look at programs that bring order to the chaos of connected atoms by arranging them in functional sections and in three dimensions.

Finding a science that has made such rapid progress in recent decades as biochemistry is difficult. Computer technology is an indispensable tool: Many biochemical processes cannot be understood until you create a three-dimensional molecular image of the active substances to illustrate their reactions.

The keyword "molecule" returns 10 entries in the Ubuntu Software Center, including one game and two drawing programs for chemical structures. But, you also will find a number of useful modeling programs, including the classic RasMol tool, the all-rounder PyMOL, the master builder Avogadro, the Jmol Java program (which runs anywhere, even in your browser), and an outsider named GChemPaint.

The most promising program, Ghemical, which not only can represent molecules but also can compute molecular orbitals, failed to make it into the test: After the install, it crashed with a number of error messages. In fact, all of the relevant forums also report installation problems with Ghemical on Ubuntu.


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    Graphics can facilitate research into chemical compounds. The chemistry software, Avogadro, has no trouble handling the third dimension and has an intuitive interface that offers more than its share of functionality.

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