BioChimeraX

What is ChimeraX?

ChimeraX is an open-source molecular visualisation tool which can be used to study proteins and DNA structures. You can install the application for free from here by choosing the latest version that matches your operating system. Molecules you wish to investigate can be found at the Protein Data Bank using this link.

ChimeraX is an incredibly useful tool for studying structures, but the user interface can be difficult to grasp. Here I will teach you how to navigate the interface and some basic commands.

Using the Drop-down Menu and Command Bar

The quickest way to manipulate your molecule of interest is through the drop-down menu but the far superior method is using the command bar. While the menu is a good way to get started, it is limited in its applications and slower than simply typing commands into the command line.

Below you can watch my short video that shows how to do some simple commands in ChimeraX that are very versatile and will be useful for the entirety of your time using this software. In this video, I use a wildtype and a mutant enzyme from the bacteria Ideonella sakaiensis to display how to use different commands on a single peptide and polypeptide protein. This enzyme is called IsPETase and has the ability to degrade PET plastic. If you wish to research these bacteria further, the research paper that first detailed its discovery can be found here and was published by Yoshida et al in 2016.

For anyone who wishes to follow the video along with written instructions, below I will detail the key commands and their uses explained:

• ‘open “file name”: this will open your file, in the video this is 8J17 and 5XJH
• ‘select #1/A’: will select chain A of your protein if you have multiple polypeptides present
• ‘select #1/A,B’: will select chains A and B of a protein (this can be continued simply by adding a comma and the next chain name)
• ‘select all’: will select all structures present
• ‘select clear’: will clear all selections made
• ‘select ~sel’: will invert selection
• ‘select :residue number, residue number’: will select specific residues (in the video it is 160, 206, 237)
• ‘view sel’: will zoom in on your selected residues/structures

Most of these commands can be achieved through the pull down menus but it is much easier to use the command bar so practice with this. If you wish to know how to use the command bar please watch my video above which will show some navigation of this.

Watch the Video