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 [1]. The process is complicated, but it works – as Figure 2 shows – if you follow the instructions [2]; 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 [3], is a good starting point for understanding the potential, especially for biology lessons in secondary schools.
RasMol, the Classic Tool
RasMol [4] 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 [5].

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 [6], 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 [7]. 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
(incl. VAT)
Buy Linux Magazine
Direct Download
Read full article as PDF:
Price $2.95
Subscribe to our Linux Newsletters
Find Linux and Open Source Jobs
Subscribe to our ADMIN Newsletters
Find SysAdmin Jobs
News
-
KDE Plasma 5.27 Beta is Ready for Testing
The latest beta iteration of the KDE Plasma desktop is now available and includes some important additions and fixes.
-
Netrunner OS 23 Is Now Available
The latest version of this Linux distribution is now based on Debian Bullseye and is ready for installation and finally hits the KDE 5.20 branch of the desktop.
-
New Linux Distribution Built for Gamers
With a Gnome desktop that offers different layouts and a custom kernel, PikaOS is a great option for gamers of all types.
-
System76 Beefs Up Popular Pangolin Laptop
The darling of open-source-powered laptops and desktops will soon drop a new AMD Ryzen 7-powered version of their popular Pangolin laptop.
-
Nobara Project Is a Modified Version of Fedora with User-Friendly Fixes
If you're looking for a version of Fedora that includes third-party and proprietary packages, look no further than the Nobara Project.
-
Gnome 44 Now Has a Release Date
Gnome 44 will be officially released on March 22, 2023.
-
Nitrux 2.6 Available with Kernel 6.1 and a Major Change
The developers of Nitrux have officially released version 2.6 of their Linux distribution with plenty of new features to excite users.
-
Vanilla OS Initial Release Is Now Available
A stock GNOME experience with on-demand immutability finally sees its first production release.
-
Critical Linux Vulnerability Found to Impact SMB Servers
A Linux vulnerability with a CVSS score of 10 has been found to affect SMB servers and can lead to remote code execution.
-
Linux Mint 21.1 Now Available with Plenty of Look and Feel Changes
Vera has arrived and although it is still using kernel 5.15, there are plenty of improvements sure to please everyone.