Introducing EasyChem, a program that generates publication-quality images of
Chemistry is one of the heavy hitters in computational science. This
has been true since the beginning, and it’s no less true today. Because
of this, several software packages specifically target this user
group. Most of these software packages focus on
calculating things within chemistry, like bond energies or protein
folding structures. But, once you’ve done the science portion, you
need to be able to communicate your results, usually in the form
of papers published in journals. And, part of the information you’ll need to
disseminate is imagery of the molecules from your work. And, that’s
where EasyChem, this article’s subject, comes into play.
EasyChem helps generate publication-quality images of
molecular structures. It should be available in the package management
repositories for most distributions. In Debian-based distributions,
you can install it with the following command:
sudo apt-get installed easychem
Once it’s installed, you can start it either from your GUI’s menu
system or from the command prompt. When it first starts, you get a
blank canvas within which to start your project.
Figure 1. You get a blank workspace when you first start EasyChem.
One of the
first things you’ll want to check is whether the option to have helpful
messages is turned on. You can check this by clicking
Options→Learning messages. With this selected, you’ll get helpful
information in the bottom bar of the EasyChem window.
Let’s start with a simple molecule like benzene. Benzene is a ring of
six carbon atoms, with every other bond a double bond. You can create this
structure by using the options at the bottom of the draw window. Making
sure that the “Add bonds” option is selected, select the “Simple”
bond from the drop-down of “Bond type”. If you now place the mouse
pointer somewhere in the window and click and drag, you’ll get a single
bond drawn. To get a ring, you need to hold down the Ctrl key, and then
click and drag. This will draw a ring structure for you.
You can set the number
of atoms to use in the ring with the “Ring size” option
in the bottom left of the window. The default is six, which is what you’ll want
for your benzene ring.
To get the alternating bond types,
select the “Edit” option at the bottom, and then you’ll be able to
select individual bonds and change their types. When you select one of
the bonds, you’ll see a new pop-up window where you can change the
details, such as the type of bond, along with
the color and the relative width if it is a multiple bond.