One of the challenges in molecular modeling and presentation is directing the attention of your viewers. Whether you’re teaching a class, giving a talk, or recording a video, clearly visualizing molecular processes—especially the dynamic ones—can be difficult.
Enter the Pulse animation effect in SAMSON, a useful tool when you want atoms, molecules, surfaces, or labels to gracefully appear and disappear. Unlike static illustrations, Pulse adds rhythm and visibility control to your scene, helping you focus attention on specific structures at precise moments.
What is the Pulse Animation?
The Pulse animation progressively shows and hides nodes in your simulation workflow. More specifically, it works on any molecular elements that have a transparency attribute—this includes structural models, visual models, meshes, and even labels. If you’re visualizing a docking process, a conformational change, or simply revealing a hidden domain in a protein, Pulse can improve clarity.
The animation operates over five keyframes:
- Keyframes 1 to 2: Nodes are fully transparent.
- Keyframes 2 to 3: Nodes gradually become visible (decreasing transparency).
- Keyframe 3: Nodes are fully visible (no transparency).
- Keyframes 3 to 4: Nodes gradually fade out (increasing transparency).
- Keyframes 4 to 5: Nodes are fully invisible again.
When to Use Pulse
Pulse is particularly helpful when:
- Comparing models before and after an event (e.g., binding or mutation).
- Focusing attention on a feature without cluttering the scene.
- Creating teaching material where progressive reveal helps understanding.
Rather than switching things abruptly on or off, Pulse makes your visualizations smoother and cognitively easier to follow. Viewers are gently guided into the visualization narrative.
How to Apply the Pulse Animation
1. First, select the nodes you want to animate. These could be a molecule, a label, or any visual model that supports transparency.
2. Then, open the Animation Panel in the Animator workspace.
3. Double-click the Pulse effect to automatically insert all five keyframes into your timeline.
Fine-Tuning the Animation
Once applied, you can adjust the timing between keyframes to match your desired pacing. For instance, extend the duration between keyframes 2 and 3 if you want a slower fade-in. You can also adjust the easing curve to control how the disappearance and appearance accelerates or decelerates, giving a more natural or more dramatic effect.
If you’re constructing a sequence showing multiple steps of a reaction or structural transformation, you can combine multiple Pulse effects to control different parts of the assembly over time.
Telling Molecular Stories, Smoothly
In molecular storytelling, visual clarity matters a lot. With Pulse, your audience feels guided rather than overwhelmed. Progressive transparency changes are a practical solution to one of the most common issues in modeling: how to focus attention in a crowded molecular scene without arbitrarily cutting things out.
To learn more, visit the Pulse animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.