When presenting molecular models—whether in research talks, educational content, or collaborative reviews—clarity is key. A common hurdle in visual storytelling is how to draw attention to important structures without cluttering the scene or drowning your audience in static visuals.
This is where SAMSON’s Pulse animation can help bring molecular mechanisms to life. Especially useful in time-dependent displays or transitions, the Pulse animation applies a transparency pulsation to selected nodes, seamlessly fading them in and out to capture attention without distraction.
Who is this for?
If you’ve ever struggled with making parts of a structure appear and disappear in a controlled fashion—a protein segment entering a pocket, changes in binding site exposure, or simply emphasizing a molecule in a dense structure—this animation tool is worth exploring.
What does the Pulse animation do exactly?
The Pulse animation operates on SAMSON nodes that support transparency, including:
- Structural models
- Visual models
- Meshes
- Labels
It guides selected elements through five keyframes:
- Keyframe 1 to 2: Fully transparent
- Keyframe 2 to 3: Transparency decreases until the node becomes fully visible
- Keyframe 3: Fully opaque
- Keyframe 3 to 4: Transparency increases, fading the node out
- Keyframe 4 to 5: Fully transparent again
What’s most helpful is that these transitions can be modified and shifted along a timeline using SAMSON’s Animator panel, so you have fine control over when and how different parts of your scene pulse into visibility.
How to Apply It
Here’s a step-by-step overview:
- Select the nodes you want to animate.
- In the Animation panel, double-click the Pulse effect.
- Adjust the five keyframes as needed by dragging them in the Animator timeline.
You can also customize how transparency changes between frames by altering the Easing curve in the Inspector. This option gives you smoother or more abrupt transitions depending on how subtle or dramatic you want the effect to be.
Why this matters
Researchers and educators alike often need to emphasize or de-emphasize components in molecular scenes. Whether highlighting binding interactions or tracing conformational shifts, the Pulse animation is especially suitable for cyclical or time-dependent phenomena. Because it requires transparency, it enables a subtle visual cue rather than a jarring hide-and-show mechanism. This smooth transition helps maintain viewer focus and avoids visual fatigue.
In summary, Pulse is a simple yet capable animation effect that can enrich molecular storytelling. It’s particularly useful when you need to animate structures that fade in and out—not just for aesthetic reasons, but to make your message clearer.
To learn more, visit the full documentation page at https://documentation.samson-connect.net/users/latest/animations/pulse/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.