When preparing molecular presentations or tutorials, it’s often important to draw focus to subtle structural changes in molecular assemblies. However, small conformational shifts can be difficult to notice—especially in large biomolecular systems. A simple technique that can make these changes more visually apparent is the Rock animation available in SAMSON.
The Rock animation causes a group of particles to perform a rocking motion around their geometric center. This motion occurs around a vector aligned with the Z-axis, passing through the centroid of the particles. While it may seem like a simple visual effect, this small movement is very effective in making otherwise static assemblies more eye-catching in videos and presentations.
Why rock a molecule?
The need to clarify a structure without overwhelming the viewer is familiar to many computational chemists and structural biologists. For example:
- You’re showing a binding site but the conformation is too subtle when viewed statically.
- You want to emphasize the shape of a protein pocket during a lecture or presentation.
- You are preparing figures or animations for a publication or explainer video.
In these cases, instead of rotating the entire molecule (which can be disorienting or mask details), a gentle rocking motion can help guide the viewer’s attention while keeping the context of the surrounding structure stable.
How to add the Rock animation in SAMSON
To use the Rock animation, follow these steps:
- Select a group of atoms or molecular components you’d like to apply the animation to. You can use SAMSON’s selection tools to define your region of interest. Learn more about selecting in SAMSON.
- Open the Animator by going to the Animation panel under the Presenting tab. Double-click on the Rock animation.
- The selected group will now rock between two default keyframes. You can reposition the keyframes in the timeline to control the speed and duration of the animation.
Customization
Animations in SAMSON support easing curves, which control how motion is interpolated between frames. To change the feel of the Rock animation—whether you want a constant pace, ease-in, or ease-out—you can edit the interpolation curve. This gives you finer control over the expression of molecular dynamics in your visuals. More on easing curves.
Example: Rocking Brd2
Interested in what this looks like in action? Here’s a public presentation using the Rock animation:
Animations like Rock are especially useful for creating educational materials where subtle orientation changes help clarify molecular organization without overwhelming non-expert audiences.
To learn more, visit the official SAMSON documentation page on the Rock animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.