When preparing scientific animations to explain molecular mechanisms or communicate results, clarity is key. A frequent challenge modelers face is: how do you selectively reveal elements of your molecular system at just the right time during an animation? Whether it’s highlighting a ligand binding site, focusing on a particular subunit, or clarifying a step in a simulation, visibility control plays a critical role in effective storytelling.
Within SAMSON, a solution already exists for this: the Shown animation effect. However, many users overlook it or confuse it with transparency-based visual changes. Let’s clarify what Shown actually does and how it can simplify the process of building clear, stepwise molecular animations—even for complex assemblies.
What does the “Shown” animation do?
The Shown animation in SAMSON explicitly sets selected nodes to be visible between animation keyframes. Unlike effects such as Appear or Pulse that may involve transitions or opacity changes, Shown operates at the visibility level itself. This makes the animation effect ideal for toggling whole components on and off instantly—without creating additional visual noise or distractions.
How to use the Shown animation
Here’s a quick walkthrough on how to apply this effect effectively:
- First, select the nodes you want to be shown.
- Go to the Animation panel in the Animator.
- Double-click the Shown effect. This will set the begin keyframe at the current animation frame.
- Advance the timeline and move the newly created keyframes as needed to match when you want the objects to appear on screen.
While this procedure might appear simple, the flexibility of moving keyframes at any time allows you tremendous control over presentation flow. This is particularly useful for building molecular training materials or presentations where timing and clarity are essential.
Why does this matter?
In collaborative environments—especially classrooms, interdisciplinary meetings, or public presentations—animations that suddenly show important residues or structural elements help maintain attention and improve understanding. For molecular biologists and chemists alike, visualizing which part of a receptor gets activated, or which substrate binds during a stepwise process, often relies more on visibility than transparency.
By including the Shown animation effect, you gain better control over what your audience sees—and when they see it. This is especially helpful where precision matters: for example, in enzyme catalysis animations, or when a molecular system is overly dense and you need to stagger visibility to emphasize each element.
Tuning the animation flow
Use the easing curve settings to fine-tune how parameters transition over time. Even though Shown is a visibility toggle rather than a fade, the easing curve may still help organize other concurrent animations with smoother flow.
To learn more, visit the full documentation page for the Shown animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.