Communicating a molecular mechanism often means going beyond static images. Whether you’re presenting a conformational change, a binding process, or a protein-ligand interaction, being able to illustrate spatial structure clearly is essential. One common challenge? Providing viewers (or yourself) with a spatial understanding of a 3D macromolecular structure without overwhelming them with too much motion.
This is where the Rotate animation in SAMSON becomes useful. A subtle rotation around the molecular centroid can instantly clarify the relative positions of atoms and domains, without needing to manipulate the model manually during a presentation or screen recording.
Why rotate?
Imagine you’re working with a multi-domain protein and want to showcase how a ligand binds into a specific site. With a slow, consistent rotation, you can give your audience a better sense of the spatial relationship between domains without switching perspectives. It also brings continuity to animations showing conformational changes by maintaining a fixed reference point.
The Rotate animation in SAMSON does just that: it rotates a selection of atoms or molecules around their geometric center along an axis parallel to the Z-axis. The result is a clean, distraction-free motion.
How to apply the Rotate animation
Here’s a simple, step-by-step process to set it up:
- Start by selecting the group of atoms or molecules you want to rotate. This can be a domain, a ligand, or even an entire protein complex. Selection is crucial, since the rotation will be computed around their centroid.
- Open the Animation panel available in the Animator. If you’re coming from an older version of SAMSON, note that the old Animation menu has been deprecated.
- Double-click on the Rotate animation effect. SAMSON will create two keyframes and apply rotation between them. The default rotation axis is aligned with the Z-axis.
- Adjust keyframes in the timeline to control the duration and speed of the rotation. You can always drag them along the animation timeline to fit your scene.
- If needed, tweak the interpolation using the Easing curve setting to make the rotation feel linear, smooth, or more dynamic.
Tip: The rotation does not change the relative positions of atoms within the selected group. It only affects their global orientation, making it suitable for exploratory visualization or presentation sequences.
Example
Here is an example of a protein complex rotating to convey its 3D structure better:
This simple animation can improve both understanding and aesthetics in your molecular modeling workflows. Combined with other animation tools like Move atoms or Rock, you can build complete molecular mechanisms and clearly demonstrate your scientific intuition.
To learn more and explore how this fits into the full animation capabilities of SAMSON, check the full documentation page:
https://documentation.samson-connect.net/users/latest/animations/rotate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform from https://www.samson-connect.net.