When presenting molecular simulations or structural changes, clarity matters. Overlapping structures, cluttered visual outputs, and abrupt transitions can confuse viewers or obscure what you intend to show. A common pain point for researchers and educators in molecular modeling is how to effectively illustrate transitions—such as binding, unbinding, conformational changes, or molecular assembly—without overwhelming the audience.
This is where the Pulse animation in SAMSON can be surprisingly helpful. By allowing selected molecular elements to smoothly appear and disappear through adjustable transparency, Pulse creates a clean visual rhythm that focuses attention on what’s changing—without introducing noise.
What the Pulse Animation Does
The Pulse animation gradually modulates the transparency of selected nodes (such as structural models, visual models, meshes, or labels), making them appear and then disappear over a defined sequence. This controlled rhythm is especially useful when you want to:
- Highlight part of a protein before or after ligand binding
- Demonstrate docking interactions
- Cycle between different conformations
- Visualize alternation between experimental and predicted data
By applying the Pulse effect via the Animation panel in the Animator, you define five keyframes that determine the transparency flow:
- Keyframes 1-2: Full transparency
- Keyframes 2-3: Gradually appear (decrease transparency)
- Keyframe 3: Fully visible (opaque)
- Keyframes 3-4: Gradually disappear (increase transparency)
- Keyframes 4-5: Full transparency again
Adjusting the positions of these keyframes lets you control timing and pacing, which is especially important when syncing with narration or other actions in a presentation.
Why This Matters
Low visibility during demonstrations can reduce the clarity of your scientific communication. The Pulse animation gives you a simple yet effective way to improve this, without needing to overcomplicate your setup. It’s also completely compatible with other animation types in SAMSON, like Show, Hide, Appear, or Flash, allowing you to build sophisticated animations from modular effects.
You can further fine-tune Pulse using the Easing curve in the Inspector panel, allowing for smoother or more abrupt transitions depending on the message you want to convey. For example, a slow ease-in can be more appropriate for transitions between large-scale states, while sharp changes can emphasize sudden events like ligand docking.
When to Use Pulse
If you’re preparing an educational video, scientific presentation, or simply sharing molecular visuals online, Pulse is a low-effort way to enhance communication. It’s especially useful when:
- You want to avoid overwhelming viewers with all structural elements showing at once
- You need to draw attention to specific parts of a model
- You’re presenting side-by-side states and want an intuitive, visual cycle
If you’ve struggled with keeping your molecular animations both elegant and informative, try integrating Pulse as a visual pacing tool. The smoother experience may help both your science and your communication efforts stand out more effectively.
To learn more about how to apply and configure the Pulse animation effect, visit the official documentation here: 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.