Presenting complex molecular mechanisms through visual animations can be a powerful way to communicate scientific insights. But sometimes, it’s not easy to find the right kind of motion to emphasize specific spatial relationships or draw attention to molecular groups. In many cases, molecular modelers want to slightly jiggle or pivot a part of their model to convey structure flexibility or simply add dynamism to their scientific visualizations—without overdoing it. That’s where the Rock animation in SAMSON can be helpful.
The Rock animation offers a modest rotational motion around the geometric center of a selected group of particles. This is particularly effective for:
- Highlighting specific domains in protein structures
- Demonstrating local flexibility regions
- Adding subtle dynamics to static models in presentations
What Does the Rock Animation Do?
The Rock effect makes a set of selected atoms rock gently around an axis aligned with the Z-direction. This means your selected particle group will pivot back and forth—a bit like a seesaw, centered on the group where the average position (centroid) defines the pivot point.
This small motion can make a big difference in focusing attention on the desired area, especially when combined with other animations. Unlike more comprehensive Rotate animations, Rock is designed to convey motion subtly.
Getting Started
To add the Rock animation in SAMSON:
- Select a group of particles. For example, you might want to emphasize the ligand-binding site of a protein.
- Open the Animation panel from the Animator interface.
- Double-click the Rock animation effect.
The animation is now added between two keyframes by default. You can position those keyframes on your animation timeline wherever necessary. The atoms will gently rock between the two frames to show a repeated motion.
Controlling Easing Curves
If you want to change the way the motion progresses over time, SAMSON lets you modify the Easing curve. This determines whether the rocking starts slowly and accelerates, or moves at a constant speed, adding an extra layer of control over the dynamics.
Example: Bringing Models to Life
An example of how the Rock animation can be used in real scientific documents can be found in this presentation of the 2BRD structure. It illustrates how a local region of a protein can be animated to communicate structural emphasis without detracting from the rest of the model.
If you frequently prepare research presentations or educational animations, Rock may be a valuable addition to your toolbox. It’s a good choice when you want to add a small amount of motion that still conveys structural intent and serves a communicative purpose.
To learn more about the Rock animation, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/rock/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.