When crafting molecular animations, researchers often want to highlight movement in one part of a system while keeping another part still for clarity or comparison. For example, during a protein-ligand docking animation, you might want the protein to remain static while visualizing the movement of the ligand. However, without tools that support this selectively restrained behavior, molecules tend to drift or move uniformly, making it hard to focus the viewer’s attention where it matters.
This is where SAMSON’s “Hold atoms” animation can offer a useful solution. This feature allows users to anchor specific atoms (or entire groups of particles) between two keyframes in an animation, making them visually fixed while the rest of the system evolves. The result: cleaner presentations and clearer interpretations when showcasing molecular mechanisms, conformational changes, or docking processes.
What does “Hold atoms” do?
The “Hold atoms” effect prevents the selected atoms from changing position between two specified frames — effectively freezing them in place over a certain time span. This can emphasize structural changes elsewhere, create contrast or provide a spatial reference point across complex simulations or presentations.
How to add the “Hold atoms” animation
- Select atoms or groups: First, use SAMSON’s selection tools to pick the atoms you wish to immobilize.
- Apply the effect: Open the Animation panel from the Animator and double-click Hold atoms.
- Adjust keyframes: Move the keyframes in your animation timeline to define when the hold starts and ends. Between those frames, the selected atoms will be kept fixed.
It’s straightforward, but the implications are powerful — especially when preparing animations for presentations, publications, or educational content where clarity is essential.
Example in practice
In the illustration below, both Move atoms and Hold atoms animations are used to create a sequence where some atoms remain still while others change position. This kind of animation is helpful to visualize localized changes without distraction from unrelated atomic motion.
When should you use this?
- Docking presentations: Keep the receptor in place while visualizing ligand movement.
- Comparative mechanisms: Fix part of the structure for easy comparisons across conformations.
- Educational animations: Reduce visual clutter for students by isolating sections of molecular motion.
You can explore examples that use this effect in curated documents on SAMSON Connect, such as:
To learn more and access detailed step-by-step instructions, visit the official documentation page for Hold atoms.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.