For molecular modelers, visually communicating dynamic behavior is essential—whether it’s for presentations, publications, or team discussions. Yet, it’s often difficult to convey subtle molecular motions effectively and understandably. One recurring challenge? Showing how groups of particles move together in a coordinated way without overwhelming or confusing your audience.
This is where the Rock animation in SAMSON can help. It offers a simple, intuitive way to emphasize the dynamic nature of molecular systems by creating a gentle rocking motion of a selected particle group around its centroid. It can be especially helpful when you want to highlight flexible protein loops, domain motions, or contrast static and mobile regions within the same structure.
What the Rock Animation Does
The Rock animation simulates a rocking movement about the center of geometry of a selected group of particles. The rocking is performed around a fixed vector that aligns with the Z-axis, so you can create a clear and consistent back-and-forth motion suitable for wide viewing angles.
This motion gives your viewers a better perception of spatial depth and can increase focus on specific parts of the model, without the total movement distraction introduced by global rotation effects.
When to Use It
- To animate flexible parts of a molecule (e.g. ligand loops or protein domains)
- To create comparisons between rigid and mobile regions
- To add subtle but informative motion without rotating the entire molecule
- To enhance visual comprehension during scientific presentations
How to Add the Rock Animation in SAMSON
- Select the group of atoms or particles you wish to animate. You can use the standard selection methods available in SAMSON. For more details, see the Selection guide.
- Open the Animator. If not visible, go to the Presenting panel to activate the Animation panel.
- Find and double-click on the Rock effect.
- Adjust the keyframes in the timeline to define the duration and frequency of the rocking motion. You can always reposition them to achieve different motion effects.
Tip: You can fine-tune how the movement interpolates between keyframes using the Easing curve. This gives you better control over the acceleration and deceleration of the animation, making it feel more natural.
Real-World Example
Here is a recorded example of the Rock animation applied to a protein (2BRD):
View this example in SAMSON Connect to explore how the Rock animation brings molecular data to life.
Whether you’re developing teaching materials, preparing a conference talk, or just aiming to better understand molecular dynamics, the Rock animation is a helpful addition to your toolbox.
To learn more, visit the full documentation of the Rock animation at https://documentation.samson-connect.net/users/latest/animations/rock/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.