Creating molecular animations can be a powerful way to communicate simulations, docking, assembly, and other molecular processes. But what if part of your structure should not move during the animation? For example, maybe you’re modeling how a ligand binds to an enzyme, and you want to keep the enzyme fixed while the ligand approaches. Or perhaps you’re animating a protein assembly, and some subunits must remain frozen to provide a reference frame.
In SAMSON, the integrative molecular design platform, there’s a simple way to fix atom positions between two keyframes: the Hold atoms animation. This animation helps molecular modelers selectively freeze parts of a structure throughout a segment of the animation—solving a common pain point for those trying to produce clear, focused molecular presentations.
What does “Hold atoms” do?
The Hold atoms animation freezes the selected atoms’ positions between two keyframes. This gives you more control over how your structures behave across time.
Without this feature, all atoms in your selection may interpolate their positions between keyframes, even if you intended them to remain static. With “Hold atoms,” you eliminate that unwanted motion.
Step-by-step: Holding atoms static
1. First, select the group of atoms you want to keep immobile for a segment of your animation.
2. Then, open the Animation panel and double-click on the Hold atoms effect. You can access the panel from the Animator interface by pressing Ctrl + 7 on Windows or Cmd + 7 on macOS.
3. This creates a Hold animation that locks the atoms’ positions between two keyframes. You can drag the keyframes to determine the duration over which the atoms will remain still.
In the example above, “Hold atoms” is used in combination with a “Move atoms” animation to show a molecule approaching a fixed target. This illustrates how different animation blocks can work together to produce a more coherent molecular story.
Tips and things to note
- You can move the keyframes at any time to adjust the timing of the hold effect.
- There used to be a dedicated Animation menu, but now all animations should be added through the Animation panel inside the Animator.
- The “Hold atoms” feature plays well with other animations—such as Move, Rotate, and Scale—letting you build layered, more meaningful animations.
Use cases
The Hold atoms animation is especially handy when creating:
- Docking animations where the receptor is fixed and the ligand moves.
- Assembly simulations where the core remains stationary while components attach.
- Comparative motion studies with parts of a structure held intact for reference.
Explore more examples that use the Hold atoms animation on SAMSON Connect – Documents, including:
Freezing specific atoms in an animation doesn’t just make your video look better—it improves clarity and helps viewers focus on what matters most.
To learn more about using the Hold atoms animation, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.