UCSF Chimera is an innovative molecular graphics system with animation capabilities.
This series of tutorials will help you to become proficient in using this software.
Before beginning to work with Chimera,
we must first understand the macromolecule data for a given entry on the Protein Data Bank.
Here we have PDB entry 1hys, the crystal structure of a reverse transcriptase enzyme from HIV.
If you scroll down on the structure summary page, you'll find the macromolecules section.
Here, each chain in the structure is given a letter code. We see here the first chain is
given the code C. However, in the brackets we see that it says "auth A" — this means that the author
of the study has labeled this chain as A. It's better to pay attention to the
labeling in these brackets because that is the labeling that you will see in Chimera.
Similarly, in the nucleic acids section, the nucleotide chains are given codes in the same way.
UCSF Chimera is available for free download for students and educators. Following the link below,
you will come to the Chimera software home page. Under Download, you will see the various
versions of the software listed. Choose the one that is most applicable for your device.
Upon opening UCSF Chimera, you will be greeted with a black graphics window with menus on the
upper left hand corner. In the bottom right hand corner, you can use the lightning bolt
icon to navigate to the blue window, which is the window you will see upon each subsequent opening.
On the right hand side, a list of previously visualized files is shown.
To open any of these files, simply click on it.
To import a new structure from the PDB into Chimera, go to File, Fetch by ID, and type
in the desired PDB identifier. Chimera will then fetch the coordinates and display the structure on
screen. Notice how some parts of the protein are represented by ribbons and others — the ligands
and specific residues — are represented by sticks. We'll explore representations further later on.
With the left mouse button pressed down, you can rotate the structure about the X and Y axes.
The same motion done far away from the structure will rotate it about the Z axis.
With the right mouse button pressed down, you can zoom the structure in and out. And with the middle
mouse button pressed down, you can translate the structure across the screen. For users with a
mouse that only has two buttons, such as an Apple Magic Mouse, you can use the left mouse button and
the Option key to achieve the same translation. Also, holding down the Shift key while performing
any of these operations makes the structure 10 times less sensitive to the operation.
Once you have found a view that you like, you can go to File, Save Image, and give your image
a suitable title. If you would like a transparent background, remember to choose the file type png
and a transparent background. When uploading to YouTube, the standard high definition resolution
is 1280 by 720 pixels. To set these dimensions for your image, uncheck this button here and
type in 1280 by 720. As a side note, images for print publication require 300 pixels per inch
of high quality image content. So if you need to print an image that is, say, 7 by 4 inches,
your dimensions — that is, your resolution — would need to be 2100 by 1200 pixels. Now,
with all these settings configured, you can save the image to a suitable location on your computer.
You can also save your session using this option here, which will retain all
of the current settings on your structure. A saved session can be restored or reopened
using this option. Finally, when you are done working with your structure,
you can close the session or quit out of the program entirely.
One other important thing to understand when you are learning to visualize proteins
is the difference between the asymmetric unit and the biological assembly.
What I have here on screen is the PDB structure 5ire, which is the structure of the Zika virus
capsid. Now if you know anything about virus structure, you'll probably realize that this
doesn't look much like a virus. That's because this is the asymmetric unit. To find the full
biological assembly, go to Favorites, Model Panel, and click Biological Unit. Now the entire viral
structure comes up and if we zoom out, we can see that it is indeed a fully functional viral capsid.
You can also see this distinction on the entry's Structure Summary page on rcsb.org. By default,
the complete biological assembly is shown here, but upon clicking one of these arrows,
we see the asymmetric unit that we had when we first rendered the structure in Chimera.