When you are working in Chimera, you will usually be visualizing protein structures. However, it is
also possible to visualize structures containing both protein and nucleic acid components.
For example, here we have the PDB entry 1hys, a reverse transcriptase enzyme from HIV.
To change the depiction of the nucleotides that the enzyme is holding,
we can go to Actions, Atoms and Bonds, and Nucleotide Objects. Under Settings we see a
panel containing the various depiction options. For example, under the side chain section,
we can change the Fill/Slab to Ladder. Now the slabs are replaced with rods as shown on screen.
Chimera contains many other useful depiction options under the Tools menu. For example,
under Depiction, we can color the structure according to a rainbow color scheme. I'm using
the default color range as shown here, but you can customize your own colors in the color editor.
When we hit Apply, the structure is colored according to the range set above, starting with
blue at each N-terminus and ending with red at each C-terminus. Because this protein contains two
chains, there are a total of four termini in the structure, two of which are highlighted on screen.
Under Tools and Depiction, we can also color by secondary structure. If we apply the default
settings, alpha helices are colored red, beta sheets purple, and coils gray. Notice that
this coloration only applies to the protein part of the structure, not the nucleic acids.
Here I have recolored the structure to a more uniform color scheme to demonstrate some of the
advanced effects that Chimera has to offer. Under Actions and Ribbon, we can activate Ribbon Edging.
This gives the ribbons thicker and more clearly defined edges. For more effect options, we can
go to Tools, Viewing Controls, and open up the Effects panel. Among the variety of effects shown
here is Depth Cueing. If we turn off Depth Cueing, the structure takes on a much flatter appearance.
You can also activate Silhouettes, which give the structure a darker outline.
You can adjust parameters such as width and color. For the most clearly defined outlines,
set the transparency under A all the way up to 1 and change the color to black.
Finally, you can turn on Shadows for a more three-dimensional appearance.
Another interesting feature to explore is the Side View. Using this feature,
you can slice through the structure to determine how much of it you will see.
You can also use Chimera to emulate the distinctive art style that David Goodsell
uses in his "Molecule of the Month" column on PDB101. In the examples shown on screen,
we can see that this style is characterized by flat lighting and the use of individual atoms
as opposed to ribbons. To achieve this style, the first step is to go to Tools,
Viewing Controls, and Lighting. Here, we can change the lighting from its default setting
to Ambient. This creates the distinctive flat look. With the lighting configured,
we can now go to Actions and show the atoms and bonds. Then we must hide the
protein ribbons by setting the selection mode to Append, selecting chains A and B,
and under Actions, choosing Ribbon Hide. With the selection cleared, we can change the atoms and
bonds depiction to Sphere. The result bears some resemblance to the art style of David Goodsell.
You can take this one step further by going to Actions, Color, and choosing By Element.
Now each atom in the protein is colored according to the standard elemental coloration scheme.