Chemistry

Study the Elements with KDE's Kalzium

Joey Bernard — Wed, 19 Jun 2019 12:00:00 +0000

I've written about a number of chemistry packages in the past and all of the computational chemistry that you can do in a Linux environment. But, what is fundamental to chemistry? Why, the elements, of course. So in this article, I focus on how you can learn more about the elements that make up everything around you with Kalzium. KDE's Kalzium is kind of like a periodic table on steroids. Not only does it have information on each of the elements, it also has extra functionality to do other types of calculations.

Kalzium should be available within the package repositories for most distributions. In Debian-based distributions, you can install it with the command:


sudo apt-get install kalzium

When you start it, you get a simplified view of the classical periodic table.

Figure 1. The default view is of the classical ordering of the elements.

You can change this overall view either by clicking the drop-down menu in the top-left side of the window or via the View→Tables menu item. You can select from five different display formats. Clicking one of the elements pops open a new window with detailed information.

Figure 2. Kalzium provides a large number of details for each element.

The default detail pane is an overview of the various physical characteristics of the given element. This includes items like the melting point, electron affinity or atomic mass. Five other information panes also are available. The atom model provides a graphical representation of the electron orbitals around the nucleus of the given atom. The isotopes pane shows a table of values for each of the known isotopes for the selected element, ordered by neutron number. This includes things like the atomic mass or the half-life for radioactive isotopes. The miscellaneous detail pane includes some of the extra facts and trivia that might be of interest. The spectrum detail pane shows the emission and absorption spectra, both as a graphical display and a table of values. The last detail pane provides a list of external links where you can learn more about the selected element. This includes links to Wikipedia, the Jefferson Lab and the Webelements sites.

Figure 3. For those elements that are stable enough, you even can see the emission and absorption spectra.

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Jmol: Viewing Molecules with Java

Joey Bernard — Thu, 24 Aug 2017 13:48:24 +0000

by Joey Bernard

Let's dig back into some chemistry software to see what kind of work you can do on your Linux machine. Specifically, let's look at Jmol, a Java application that is available as both a desktop application and a web-based applet.

You can use Jmol to help analyze the results you get from other software packages that actually calculate the chemical effects you are researching. It can read in dozens of different file formats, and you can use it to visualize everything from small molecules to huge macromolecules, like proteins. You also can visualize crystals and orbitals. You even can visualize animated events, such as chemical reactions and molecular vibrations.

Most Linux distributions should have Jmol available within their package management repositories. For example, you can install it on Debian-based distributions with this command:


sudo apt-get install jmol

If you want to use the latest and greatest version, download it from the main project website. The download comes as a simple zip file containing everything you need to run Jmol. You also will need to install a Java virtual machine in order to run Jmol.

If you installed Jmol from the package manager, you probably will have a script available that will make running Jmol easier. If you install it from the binary zip file, you will need to run it manually by calling Java and using the JAR file as a command-line option.

When you first start Jmol, you'll see a blank screen, ready for input. Across the top is a series of icons allowing for easy access to the key functions available within Jmol. If you already have data files to analyze, you can use them. Otherwise, you may need some sample files in order to play with the functionality available.

Figure 1. When you first start Jmol, you get a blank workspace ready for your work.

The binary distribution doesn't include any sample files in order to save on download bandwidth; however, several sample data files are available from the main website. You can get the entire set by downloading a snapshot of the source files. In the examples for the rest of this article, I'm using several of the sample data files available from the source snapshot download.

The simplest example is just to load a data file and see what it looks like. Figure 2 shows what you get when you load the sample file Jmol-datafiles/gaussian/phenylnitrine.g94.out.

Figure 2. The basic display you get when you load a molecule is a ball and stick display.

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Chemistry on the Desktop

Joey Bernard — Thu, 23 Mar 2017 15:49:41 +0000

by Joey Bernard

For this article, I thought I'd introduce another chemistry application—specifically, BKChem, a free chemical drawing program. As opposed to many other chemistry applications, BKChem provides both a nice GUI for constructing molecules and a set of chemical analysis tools to look at the properties of the newly constructed molecule.

Most distributions should have a package available to make installation easier—for example, Debian-based distributions can install BKChem with the following command:


sudo apt-get install bkchem

Once BKChem is installed, you can start it either from the menu entry or by executing the command bkchem from a terminal window.

When it first opens, you'll see a blank screen where you can start your chemical construction.

Figure 1. When you first start BKChem, you get a blank canvas to start building your molecule.

If you have a previously created molecule, you can load it by clicking the File→Load menu item, which will load the data into a new tab, or you can click the File→Load to the same tab menu option to load it into the currently active tab.

BKChem also can import data from other file formats. If you click File→Import, you'll see that you can import files with CML, CML2 or Molfile formats.

If you want to start by building your own molecule, several menus of building blocks are available. They are laid out as a pair of rows, just below the menu listings at the top of the window. The top row of icons selects which list of icons will be available in the second row. The first icon in the first row is simply an arrow, allowing you to select objects within your molecule so you can edit their properties. The next icon pulls up the row of drawing elements where you can start to draw your new molecule.

There are several choices in terms of line thicknesses, styles and bond angles, and you can create a chain of elements simply by clicking on the end of an existing line segment.

Once you have the basics of your structure laid out, you'll want to edit the details next. To do this, click on the first icon again (captioned with "edit"), and then click on the structure element you want to edit. This is where having a proper mouse is a must, as you need to click with the middle button on your mouse to pull up the edit panel.

Figure 2. You can edit an element by clicking the middle mouse button. The menu you get depends on the type of element you are editing.

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