When preparing molecular animations for presentations or educational videos, one challenge comes up again and again: how to reveal molecular components at exactly the right moment. Whether you’re illustrating the binding of a ligand, the assembly of a complex, or a transition in a protein conformation, there’s often a need to introduce new atoms or structures mid-animation without switching to another scene or using overly complex transparency effects.
This is where the Show animation in SAMSON can be particularly useful. It allows you to make selected nodes (atoms, molecules, groups, representations, etc.) appear explicitly at a chosen time point in your animation, and remain visible until the end of the presentation. This animation works by controlling the visibility of nodes, not their transparency, making it clean and effective.
Why use Show instead of Transparency or Appear?
It might be tempting to use other tools—like changing transparency or using the Appear animation—to introduce your elements to the scene. However, “Show” simplifies visibility transitions by handling the “hidden” and “shown” states in one controlled sequence. You don’t need to sequence separate “Hidden” and “Shown” animations manually.
How it works
Adding the Show animation in SAMSON is straightforward:
- Select the nodes you want to appear during your animation.
- Double-click on the
Showanimation in the Animation panel of the Animator. - Adjust keyframes to define when and how the nodes appear on screen.
The animation consists of three keyframes:
- Keyframe 1 to 2: nodes are hidden.
- At Keyframe 2: nodes become visible.
- Keyframe 2 to 3: nodes remain visible.
You can reposition these keyframes freely along your timeline to control when the structures appear.
Example in action
The following animation shows a simple use case of the Show animation applied to a molecular structure so that part of the system is only revealed mid-sequence:
Fine-tuning the animation
To control how quickly the “appearance” feels to the viewer (e.g., snappy or smoothed-in), you can use an easing curve. This gives you control over the motion and timing of your presentation elements. Although the visibility transition is binary (something is shown or not), the timing can give a more polished feel to your animation.
When to use it?
The Show animation is useful in a variety of contexts, especially when you want to:
- Introduce ligands or cofactors at a specific step in a mechanism.
- Emphasize molecular components one by one for educational purposes.
- Simplify complex animations by avoiding separate hidden/shown transitions.
- Create a more guided narrative in your molecular movie or slideshow.
If you often find yourself manually toggling visibility for different parts of your system in your timeline, this tool will likely reduce that overhead and help keep your animation workflow clean and replicable.
To learn more, visit the full documentation page for the Show animation: https://documentation.samson-connect.net/users/latest/animations/show/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.