In Chimera, you can animate structure translations and rotations in X-Y-Z,
changes in the representation of ribbons and atoms, changes in opacity and color, and more.
In this tutorial, we will explore some of these capabilities by creating a short animation
with the hemoglobin structure 4hhb.
Before we begin to animate, it is important to obtain the correct dimensions for the graphics
window. If you're uploading to YouTube, you'll want your dimensions to be of the ratio 1280 by
720. To set this ratio for the graphics window, type into the command line: windowsize (all one
word) space 1280 space 720 — and press Enter. Now this is a relatively small window to work in,
so feel free to scale up the dimensions if needed. For this tutorial, I'll be scaling
up by a factor of 1.5, which will make the graphics window have dimensions of 1920 by 1080.
Now we can go to Tools, Utilities, and Animation to access the animation
interface. We will be using this interface to create snapshot scenes called keyframes,
each containing a different depiction state of the structure. Once we arrange these keyframes
in the timeline, Chimera will transition smoothly between them to create the animation.
At this point, it's also worth noting that Chimera's animation runs at a rate of 24
frames per second. This value will become an important conversion factor later on.
To create our first keyframe, we'll take a snapshot of the structure in its default state
using the green "+" icon. Next, we're going to set up a color change by going to Actions,
Color, All Options, and selectively coloring the ribbons green. Now we'll take a snapshot of
the result to create the second keyframe. It is also possible to update keyframes once you have
created them. Let's say that you want to color the protein ribbon something other than green.
To do this, we first make the desired change and then right-click on the corresponding
keyframe and select Update. Now that keyframe contains the change made in the graphics window.
For our final scene, we are going to zoom into a heme group by first selecting chain B,
then changing the selection mode to Intersect, and finally selecting Heme.
Then under Actions, we can focus in on the heme group, clear the selection,
and take another snapshot to create the final keyframe.
It is now time to begin arranging the keyframes in the timeline. To do this, we drag them in one
by one. Notice the number that appears at the bottom as we drag them in — that number denotes
the number of frames currently contained in the animation. Recalling that Chimera runs at a rate
of 24 frames per second, we see that the current duration is about 3 seconds. By right-clicking
on the keyframe and selecting Properties, we can set the transition length precisely.
This value denotes the number of frames between the current and preceding keyframes.
Now the color change will take exactly 3 seconds to complete.
Similarly, we will allow 3 seconds for the zoom transition
by again going to Properties and then setting the frame number to 72. In the timeline,
the three keyframes are equally spaced, in accordance with our frame number settings.
Finally, we can add a 360 degree rotation to the animation
by dragging the Roll action into the timeline. We don't want the rotation to be too fast though,
so we will allow 7 seconds by going to Properties and setting the frame number to 168.
Now we are ready to export the animation. To do this, we click the red and gray Record button.
Now we can give our animation a suitable name such as 4hhb-animation.
Next we need to select the file format — here, I'll go with the default H.264.mp4.
Finally, we hit record and wait for the animation to render.
With the export complete, we can now view the finished animation.