Creating clear molecular presentations often means finding the right balance between visual aesthetics and conveying scientific meaning. One common challenge many molecular modelers face is how to highlight specific structures or changes without overwhelming the viewer. Whether you’re preparing an animation for a scientific presentation or a classroom lecture, managing visibility and transitions between elements can be tricky.
The Pulse animation in SAMSON offers an elegant way to address this. It helps you draw attention to specific molecular structures by controlling their appearance and disappearance through transparency over time. This animation is especially useful when you want elements to smoothly fade in and out — ideal when emphasizing or cyclically displaying regions within a complex system.
What Does the Pulse Animation Do?
The Pulse animation applies to nodes that support transparency, such as:
- Structural models
- Visual models
- Meshes
- Labels
It works by gradually decreasing and increasing the transparency of these elements, making them appear and disappear rhythmically — hence the name “Pulse.” This is particularly helpful when trying to:
- Compare structural changes over time
- Focus on specific sites in large biomolecular systems
- Highlight dynamic features in molecular simulations
How to Use It
- Choose the nodes you want to animate.
- Open the Animation panel inside the Animator in SAMSON.
- Double-click the Pulse effect to apply it to the selected nodes.
The Pulse animation is composed of 5 keyframes by default:
- 1 → 2: Nodes remain fully transparent.
- 2 → 3: Nodes gradually become visible.
- Keyframe 3: Nodes are fully visible (opaque).
- 3 → 4: Nodes gradually disappear again.
- 4 → 5: Nodes return to being fully transparent.
You can adjust the position of the keyframes to synchronize the pulsing effect with other animations or time-based events in your molecular scene.
Customizing the Transition
By default, the Pulse animation uses a linear transition, but SAMSON gives you full control over how transparency changes between the keyframes. You can fine-tune the behavior by editing the Easing curve, allowing for effects such as slow fade-ins or sudden changes.
These kinds of easing methods can enhance the rhythm of molecular animations, especially if you apply the Pulse effect to multiple nodes with staggered timing, creating a ripple-like reveal through your structure.
Visualization Example
Below is an example of the Pulse animation applied to a molecular system. Nodes fade in and out, giving viewers a breathing-space transition effect that promotes focus and clarity:
Is It Worth Using?
Definitely, especially if you’re looking to produce more engaging and less cluttered animations. Even in highly complex systems, the Pulse animation helps reduce visual overload by modulating the presence of selected molecules or annotations.
To learn more about working with the Pulse effect, visit the official documentation page:
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.