Here we have the PDB entry 3WU2. This is a structure of the Photosystem II complex that
plays a pivotal role in photosynthetic light capture and water splitting. In this tutorial,
we will explore this structure using some of the MolStar (Mol*) Viewer's animation capabilities.
Under Export Animation, there are a number of animation modes to choose from.
The one we will explore right now is Camera Spin. The default parameters
for duration and speed will produce one 360º rotation that takes 4 seconds to complete.
For now, let's proceed with these settings to create our first animation.
Before we hit Render though, we need to adjust the resolution under the Camera icon.
For this tutorial, I'll be going with dimensions of 1280×720,
which are good dimensions for uploading to YouTube. Now you may have noticed that
the resolution displayed in the animation panel does not match the resolution set above. That's
because we have Auto-crop turned on. Once we turn it off, the resolutions match up.
Now we can render the animation and wait for it to export. With the rendering complete,
we can hit Save Animation to receive the file into the Downloads folder.
And here is the finished animation.
Returning to the Mol* Viewer, we will now cover the customization of the Camera Spin parameters.
Let's say we want the structure to complete two full 360º rotations instead of just one.
To do this, we will adjust the Speed slider to 2. However, notice that the duration is still
at the original 4 seconds. This means that the spin cycles are probably going to be too fast.
To solve this problem, we can set the Duration slider to 8 seconds,
preserving the default ratio of 1 rotation per 4 seconds.
In your own projects, feel free to experiment with different ratios to create animations of
varying rotational speed. For this tutorial, I'll move ahead with the current settings
by clicking Render, and downloading the file once the export is complete.
Now the structure makes two full rotations, but at the same speed as before.
It is also possible in the Mol* Viewer to animate specific parts of a protein structure.
In this next animation, we will visualize Photosystem II's active site, which is where
the water splitting reaction occurs. To do this, we start by unrolling this drop-down menu and
selecting Item 20 — the calcium-manganese-oxygen cluster. Then, upon clicking OEX as shown,
a rendering of the cluster appears. To make this depiction a little clearer,
we can go under Components and hide the cartoon ribbon by clicking the "eye"
icon. If we want, we can also remove some of these interactions by going to these bar controls,
selecting Non-covalent Interactions, and turning off the hydrogen bonds.
Once we land on a good orientation for the active site, we can optimize the animation
parameters. There is a lot of detail to take in here, so we should choose a
moderate pace for the rotation — something like 7 seconds for the full 360 degrees.
As before, we hit Render and download the resulting file.
And here is the completed animation.
Finally, I will demonstrate another animation capability that the Mol*
Viewer has to offer — Spin Structure. Instead of producing a simple rotation around the y-axis
(like Camera Spin), this mode will turn the structure end-over-end.
The default duration is a bit fast, so we will extend the slider to 5 seconds.
As before, we click Render, and then download the exported file.
And here is the finished animation.