When visualizing molecular designs, motion tells a powerful story—highlighting transitions, conformational shifts, or dynamic interactions with clarity that static images can’t match. But creating smooth, accurate animations can often seem like a hurdle, especially when working with molecular systems where atom positions matter.
One effective solution in SAMSON is the Move atoms animation, which lets you interpolate atomic positions between keyframes. This capability is particularly valuable for creating simple and intuitive animations without requiring deep scripting or video editing knowledge. In this blog post, we’ll focus on the highly practical task of adding and managing keyframes using this feature.
What’s the challenge?
You’ve prepared a structure and want to show a transformation—a subunit sliding, atoms rotating, or a folding motion. Manually moving atoms over time is time-consuming and error-prone. What you need is a way to define only the important moments (the keyframes), and let the software interpolate the positions in between.
How keyframe animation helps
Using the Move atoms animation effect in SAMSON, you can:
- Select atoms and define initial positions (first keyframe).
- Move the playhead, reposition the atoms, and create a new keyframe.
- SAMSON then smoothly interpolates motion between these frames.
This makes it much easier to communicate molecular mechanisms or prepare engaging scientific presentations to share with colleagues or in lectures.
Step-by-step: Creating a keyframed animation
1. Start by selecting the relevant atoms you’d like to animate. You can use SAMSON’s selection tools for precision.
2. In the Animator’s Animation panel, double-click on the Move atoms effect. This action sets your first keyframe.
3. Move the frame indicator in the animation track to where your second keyframe should be. Then, reposition the atoms using the Move editors, Twister editor, or directly via transformation if you prefer.
4. A new keyframe will automatically be created when a change is made. You can keep repeating this process to define more stages in your animation.
Editing and fine-tuning your animation
Keyframes can be freely moved along the timeline to adjust timing. If you misplace one, just right-click it in the Animator’s Track view and select Remove keyframe.
Customization
The Move atoms animation is more than just linear interpolation. You can adjust the look and feel of your animation by tweaking the Easing curve and enabling/disabling smoothing directly in the Inspector.
When this feature is most useful
This animation feature is ideal when showing:
- Subtle conformational changes in proteins
- Nanotube elongation or bending
- Binding/unbinding simulations
- Transitions in nanostructured materials
By leveraging keyframes, scientists and educators can produce clear, compelling visualizations much faster than stitching together screenshots or relying on rendering tools with steep learning curves.
To learn more and explore additional examples and controls, visit the full documentation at https://documentation.samson-connect.net/users/latest/animations/move-atoms/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.