Molecular modelers often face the challenge of presenting their work in a clear and intuitive manner. When creating animations of molecular systems—whether for presentations, publications, or teaching—controlling *when* specific atoms or groups become visible is essential. Flickering atoms or unclear transitions can confuse viewers, especially those unfamiliar with the molecular system being shown.
This is where the Show animation in SAMSON becomes particularly useful. It provides an intuitive way to make nodes (atoms, molecules, groups, etc.) appear at a specific point in your animation timeline and remain visible until the end. Unlike transparency tweaks—which can be subtle and confusing—the Show animation offers a sharp, unmistakable change in visibility. ✨
Let’s walk through how to use the Show animation efficiently, and how this simple feature can help improve your molecular presentations.
What does the Show animation do?
Using visibility (not transparency), the Show animation makes selected nodes appear at a chosen keyframe and remain visible until the end of the animation. It helps you build up your scene incrementally, which is great for storytelling—especially in biochemical mechanisms or assembly processes.
Why is this useful?
Suppose you’re showing how a protein complex assembles. Rather than starting with a cluttered view of all components, you can use the Show animation to introduce each component one by one. This results in a cleaner, more engaging experience for the viewer.
How to add the Show animation
Step-by-step:
- Select the nodes you want to appear at a certain time in the animation.
- Open the Animation panel in the SAMSON Animator.
- Double-click the Show effect to apply it to the selected nodes.
This effect comes with 3 keyframes:
- Between keyframes 1 and 2: nodes stay hidden.
- At keyframe 2: nodes appear.
- Between keyframes 2 and 3: nodes remain visible.
You can move keyframes freely to control the exact timing of appearance. For example, you might want a ligand to appear just after a protein pocket opens up, or certain residues to become visible only after a structural rearrangement.
Customizing motion
If you’re not a fan of abrupt changes, you can adjust how the animation behaves between keyframes using the Easing curve. This can subtly influence how smooth the visibility transition feels, offering a more refined look.
Note on recent updates
In previous versions of SAMSON, animations were added via an Animation menu. If you’re using the latest version, make sure to go through the Animator and its Animation panel, as this menu is no longer available. All presentation actions can now be accessed directly there.
When not to use it
Although the Show animation is great for visual onset of structures, if you want to fade objects in or out smoothly, using the Appear or Disappear animations may be more appropriate. Also, for dynamic highlighting, effects like Flash or Pulse could be worth exploring.
To learn more, visit the full Show animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.