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.
What the Programs Offer
Chemical formulas are something like the technical language of chemistry. Originally, scientists used the molecular formula, a simple string of letters and numbers for the elements and their numbers in the molecule. Later on, the two-dimensional structural formula yielded significantly more information about the molecule, such as the existence of single and double bonds.
Visualization programs now add scale to the structural formula (Figure 1). The atoms appear in their correct positions and can be viewed from different directions. Additionally, depending on the program that is used, you can also display molecular surfaces, functional components, or electron density maps. What looks a little like technical overkill in the simple ethylene molecule in Figure 1 turns out to be extremely helpful with complex molecules such as DNA.
Representing the electron distribution around the nuclear framework of the molecule is another excellent capability of molecular visualization: If you want to understand how electrostatic attraction and repulsion processes act within the molecule, an electron density map is a big help. To generate it, you can call on the Electron Density Server at Uppsala University . The process is complicated, but it works – as Figure 2 shows – if you follow the instructions ; I generated this image with PyMOL.
The following brief summary highlights some applications, but they will not reveal their impressive visualization capabilities until you perform your own experiments. If you are interested, you should check out the power of moving molecular images yourself. Specifically, the DNS representation on the Biomodel site by Angel Herráez at Universidad de Alcalá, Spain , is a good starting point for understanding the potential, especially for biology lessons in secondary schools.
RasMol, the Classic Tool
RasMol  was the first molecular visualization program for Linux (Figure 3). The Gtk-based version discussed here (version 2.7.5) impresses by not being overly complex and allowing quick switching from one view to the next. Rotate and zoom processes are intuitive after a short time, and RasMol tutorials are available online .
Simultaneous loading of multiple molecules is possible. After selecting the visible molecule, you can change its appearance and position, thus illustrating the interaction of several molecules in synthetic processes, for example.
RasMol runs not only on Linux, but also on Mac OS X and Windows – but only on the desktop. This means you cannot create web tutorials, which are so meaningful in education.
Jmol, the Multipurpose Tool
Jmol, written in Java , can be used both on the desktop and integrated with HTML pages as an applet. Thus, it allows for interactive tutorials that let you put together ideal interactive learning units for upper-level classes.
Many great examples relating to DNA are available online from the Spanish Biomodel website I mentioned before . Thanks to Java, Jmol runs as a desktop application on almost any operating system, offering a clear-cut, intuitive user interface (Figure 4).
Buy this article as PDF
Linux Magazine will include the best of both magazines.
Popular open source encryption tool is vulnerable to attack
New “Yakkety Yak” edition emphasizes cloud and servers
Google finally enters the phone hardware business.
Innovative system adds a hard drive and Ubuntu Core to the RPi for an IoT hub.
Linux is two weeks younger than we thought!
The Apache Software Foundation considers retiring OpenOffice
Adobe won’t kill the plugin in 2017
Linux Foundation's big event celebrates the 25th anniversary of Linux