Welcome! This orientation will help you navigate the 3D molecular models for BC401 (Fundamentals of Biochemistry) at Colorado State University.
Use the below the text box to navigate between articles.
If you are viewing this on a large screen, you can also use the to navigate between articles. Navigating beyond the extent of the articles will load the adjoining page, or take you back to the homepage once you reach the end of the chapter.
There are links to the and , as well as links to return to the .
Each article is accompanied by a molecular model rendered by .
Currently, ATP is shown in the JSmol viewer. JSmol is rendering the molecular data as a ball-and-stick model in CPK colors. This is the default for newly-loaded files.
Navigating between articles will write new commands to JSmol. Now, the ATP molecule is shown as a spacefilling model, with the modeled radius of each atom representing the van der Waals radius.
Many articles will include buttons that will alter the model to highlight important concepts. For example, let's spin on and off to admire the geometry of the molecule. Now between spacefill and ball-and-stick models.
Practice moving the molecule by clicking and dragging the cursor over the JSmol window. Releasing the cursor (or your finger) while dragging will cause the model to spin along the vector (including magnitude) of your gesture.
There are countless keyboard shortcuts to move, zoom, rotate, select, and more. You can find a full list of commands by clicking here.
Everyone learns differently. Although this site is designed to provide a framework for teaching biochemistry, it also allows you to explore well beyond the subject material. JSmol is an extensive and powerful tool, and the goal of this site is to allow you to maximize its potential.
Click on the next to the viewer to reveal the toolbar.
The button, found within the toolbar, will restore the settings that accompany each article. This may include orienting the molecule and forcing spin on or off, and can be helpful if you get carried away with the settings in the toolbar.
The button will reset all the settings applied to the model, including the article defaults.
We will explore the toolbar in greater detail on the next page.