When creating molecular graphics for presentations, publications, or videos, motion plays a key role in storytelling. Whether you’re explaining the binding mechanism of a drug, highlighting a conformational change, or simply making your scene more engaging, well-crafted animations can help others quickly grasp complex molecular information.
That said, many molecular modelers struggle with one frustrating pain: making molecules rotate meaningfully around a well-defined point. It’s a subtle detail, but critical—an arbitrary spin can confuse viewers or introduce misleading cues. Fortunately, this is where SAMSON’s Rotate animation can help in a very precise and intuitive way.
Rotating with purpose
The Rotate animation in SAMSON lets you rotate groups of atoms or molecules around their geometric center—the centroid of the selected particles. What’s more, the rotation axis is automatically aligned with the global Z-axis, which ensures consistency in your scenes, especially useful for multi-step animations or comparative visualizations.
This is particularly useful when presenting cyclic molecules, protein channels, or any structure where a centralized, consistent pivot is visually important. Instead of arbitrary spins, viewers observe a meaningful rotation that respects molecular geometry.
How to apply it
- Select a group of atoms or molecular structures you want to rotate. You can select them using SAMSON’s selection tools.
- Open the Animation panel in the Animator interface.
- Double-click on Rotate in the list of available animation effects. That’s it—SAMSON automatically calculates the centroid and applies the rotation.
You can adjust the time between the two keyframes to control how fast or slow the rotation occurs, or reposition the keyframes altogether. Additionally, the Easing curve allows you to control the interpolation style — making motion linear, accelerating, or smooth decelerating.
Why this matters
Beyond aesthetics, purposeful rotation serves:
- Education: Helping students or peers understand spatial conformations by controlling what they see and how they perceive motion.
- Presentations: Animations that rotate around a clear center give a professional and intentional look to your molecular scenes.
- Clarity: Highlighting symmetrical features or allosteric pathways—some of which may only be apparent when viewed at the right angle or during motion.
In the example above, atoms rotate smoothly around their midpoint, providing a seamless way to inspect their structure from all sides. This can be useful, for example, when showing a ligand in the pocket of a larger macromolecule—you can reveal occluded details that would otherwise be hidden from a static viewpoint.
While the Rotate animation is now handled via the Animator’s panel (the old Animation menu has been removed), this new workflow provides more flexibility and direct control, especially when planning multi-step animations.
Want to dive deeper into this feature? Explore the full documentation for the Rotate animation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.