When you prepare molecular animations to explain your research or present your findings, the clarity of visualization often makes the difference between confusion and understanding. A common challenge faced by many molecular modelers is: how to intuitively highlight structural features or transitions in a way that keeps the viewer’s attention.
One particularly effective solution is to add a consistent rotating motion to molecular fragments. This simple effect can dramatically improve perception by providing spatial context. In SAMSON, this is made possible via the Rotate animation effect found in the Animator panel.
Why Rotate?
Rotating a group of particles around their centroid not only showcases the 3D structure more effectively but also creates a natural focal point for viewers. Whether you’re rotating a ligand in a binding pocket or an entire polymer chain, this motion introduces depth and makes the presentation more dynamic—ideal for presentations, publications, or teaching scenarios.
How It Works in SAMSON
The Rotate animation rotates the selected particles around their geometric center (centroid), along a vector aligned with the Z-axis. This ensures predictable and intuitive motion, ideal for consistent effects across multiple visualizations.
Steps to Add a Rotate Animation
- Select the group of particles you want to animate. This could be any atoms or molecular group in your model. See the selection guide if you need help.
- In the Animator, find the Animation panel and double-click
Rotate. - SAMSON will automatically add two keyframes. Between these, the selected particles will rotate around their centroid.
- You can now move or stretch the keyframes along the timeline to control the duration and sequence of the rotation.
Customizing the Rotation
You’re not limited to a fixed interpolation between keyframes. SAMSON allows you to adjust the Easing curve, which defines how parameters like rotation speed change over time. For example, using an ease-in-ease-out curve will produce a smoother spin that starts and ends gently.
Even after applying the rotation, you can always:
- change the time range of your animation
- tweak the keyframe positions for timing control
- add other effects like zoom or hold to combine animations
Note on Interface Changes
If you’ve used a previous SAMSON version, you may remember an Animation menu. This menu has been merged into the Animation panel in the Animator interface for a more unified workflow.
When to Use Rotation Animations
If you’ve ever tried to present a still image of a molecular docking result and felt it lacked clarity, or if you’ve needed to show how a protein conformational change appears in 3D, the Rotate animation can offer the extra touch to make complex spatial relationships obvious. It’s especially useful for:
- Orbiting around a molecule to show symmetry or spatial arrangement
- Highlighting interaction regions by slowly revealing surfaces
- Creating looping demo clips for educational use
To learn more about the Rotate animation in SAMSON, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/rotate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.