Four 3D molecular visualizers compared
Avogadro, the Master Builder
Avogadro [8] does not aim to represent known structures, even though the application can do so; instead, you build your own molecule with Avogadro without having to know the coordinates of the individual atoms.
To begin, you just start to draw the rough structure from atom to atom. Then, you can start optimization mode and let Avogadro optimize the geometry of the molecule in line with energetic considerations: The lower the binding energy, the more dense the molecule is in the real structure. After composing the molecule, you then measure it and tell Avogadro to output the atom coordinates (Figure 5).
PyMOL, the All-Rounder
PyMOL's [9] capabilities are demonstrated in Figure 2; the program computes and shows the electron density incrementally in line with the instructions [2]. PyMOL is as complex as it is powerful and consists of a script window and an image window, where it shows the computed image.
If you load multiple images, such as the molecule and the electron density space, as in Figure 2, then you can label the individual views by using the buttons labeled to the right of the image window. In my experience, masterful use of the PyMOL program is unlikely to be achieved without occasionally referring to the manual [10] – performance has its price.
GChemPaint, the Outsider
Strictly speaking, GChemPaint [11] is not in fact a visualization program. It made its way into our lab by virtue of one neat property: It can read data in the popular PDB molecule format of the Protein Data Bank [12], a freely accessible database that contains resources contributed by international biologists and biochemists in the form of 3D structures of proteins and nucleic acids.
The GChemPaint program shows the structural formula directly from the PDB coordinate files. This structural formula is then more useful in scientific documentation than a 3D visualization – as long as the molecules are not too big (Figure 6).
« Previous 1 2 3 Next »
Buy this article as PDF
(incl. VAT)
Buy Linux Magazine
Subscribe to our Linux Newsletters
Find Linux and Open Source Jobs
Subscribe to our ADMIN Newsletters
Support Our Work
Linux Magazine content is made possible with support from readers like you. Please consider contributing when you’ve found an article to be beneficial.
News
-
TUXEDO Computers Unveils Linux Laptop Featuring AMD Ryzen CPU
This latest release is the first laptop to include the new CPU from Ryzen and Linux preinstalled.
-
XZ Gets the All-Clear
The back door xz vulnerability has been officially reverted for Fedora 40 and versions 38 and 39 were never affected.
-
Canonical Collaborates with Qualcomm on New Venture
This new joint effort is geared toward bringing Ubuntu and Ubuntu Core to Qualcomm-powered devices.
-
Kodi 21.0 Open-Source Entertainment Hub Released
After a year of development, the award-winning Kodi cross-platform, media center software is now available with many new additions and improvements.
-
Linux Usage Increases in Two Key Areas
If market share is your thing, you'll be happy to know that Linux is on the rise in two areas that, if they keep climbing, could have serious meaning for Linux's future.
-
Vulnerability Discovered in xz Libraries
An urgent alert for Fedora 40 has been posted and users should pay attention.
-
Canonical Bumps LTS Support to 12 years
If you're worried that your Ubuntu LTS release won't be supported long enough to last, Canonical has a surprise for you in the form of 12 years of security coverage.
-
Fedora 40 Beta Released Soon
With the official release of Fedora 40 coming in April, it's almost time to download the beta and see what's new.
-
New Pentesting Distribution to Compete with Kali Linux
SnoopGod is now available for your testing needs
-
Juno Computers Launches Another Linux Laptop
If you're looking for a powerhouse laptop that runs Ubuntu, the Juno Computers Neptune 17 v6 should be on your radar.