Visualizing Molecules with EasyChem

Joey Bernard — Thu, 24 May 2018 13:08:08 +0000

Introducing EasyChem, a program that generates publication-quality images of molecular structures.

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.

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LyX Devs Release First 2.0 Release Candidates

Michael Reed — Mon, 04 Apr 2011 13:00:00 +0000

by Michael Reed

Considering that the dev team has been working on it for about two years now, the LyX 2.0 release candidates are starting to appear relatively quickly (RC2 at time of writing). The file format is now fairly fixed and should now be forwards compatible with all later versions, so this might be a good time for LyX die hards to check out 2.0, if they haven't already.

If you are an existing LyX user and you're building one of the release candidates from source, consider using something like:

./configure --with-version-suffix=2RC

This allows you to run the RC completely independently of other installed versions.

LyX is one of my favorite pieces of software, but I sometimes hesitate to recommend it as it's not for everyone. Let's just say, it is easy to use, once you learn how to use it. Even then, it's aimed at technically minded people.

In a nutshell, it's a writing tool in the form of a kind of text editor that outputs the finished document via a LaTeX back end. It's main target is academic writers, but particularly in light of some of the new improvements, it ought to be better known to all writers who want to separate content from layout. LyX 2.0 is an improvement of earlier versions of the software rather than a complete departure, which will please veteran users of the program.

Hurrah! LyX now sports a real time spellcheck that underlines misspelled worlds. The traditional step-by-step spell checker still exists, but it is now implemented as a sidebar rather than a free-floating window. The thesaurus now makes use of a different back end, allowing it to be multi-lingual. Unfortunately, for the moment, it uses its own window rather than a sidebar.

LyX 2.0RC1 in action. To the left, the document navagation sidebar in one of its many modes. To the right, a the new advanced search and replace sidebar. In the centre, something complicated taken from the documentation files.

A few of the new features make user of sidebars, improving usability. LyX has an advantage here as it isn't a word processor and can re-flow the text when sidebar is activated.

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