Section 2: Simplifying the view

As you have probably realised, it is difficult to see very much with this default (ball and stick) view of the structure. For this reason, Geneious provides a number of tools that manipulate the display.

Styles

Click on the Style button and you will be offered a number of alternatives. Each applies to the selected atoms only but for the moment all atoms are selected. If not, click on the Select box to the far right and click all.

Try these styles out for yourself.

Colors

Another useful feature is the ability to color structures.

Try combinations of styles and colors.

Select Backbone and Monomer. This is effective at showing the start and stop of the polypeptide chain. Combine this coloring with rocking the structure and you will have a good idea of how the linear primary sequence folds into the final tertiary structure.

Select Cartoon and Structure. Now you can clearly see the position of the secondary structure elements. You can see the α-helices and how the β-strands combine to form β-sheets.

Effects

Geneious provides some effects to improve the appearance of your structure or make it easier to see features.

Section 3: Selecting parts of the structure

Section 4: Showing useful information