Visualizing molecular processes often involves complex scenes with multiple components—such as proteins, ligands, meshes, and labels. But when everything appears at once, important details can get lost. One way to guide viewers through such rich content is to control when and how elements appear and disappear. This is where the Pulse animation in SAMSON can make a difference.
The Pulse animation gradually reveals and then hides nodes, helping structure your molecular visual story. Rather than presenting all elements simultaneously, you can focus your audience’s attention on key actors at the right moment—especially useful during presentations or video creation.
What Does Pulse Do?
The Pulse animation acts on nodes that have transparency attributes. These can be structural models, visual models, meshes, or labels. Instead of instantly appearing or disappearing, the selected nodes fade in and out smoothly. This can serve to emphasize transitions or highlight processes that unfold over time, even when they are otherwise static models.
Here’s how the animation progresses over 5 keyframes:
- Keyframes 1–2: Nodes are fully transparent
- Keyframes 2–3: Nodes gradually appear (transparency decreases)
- Keyframe 3: Nodes are fully visible
- Keyframes 3–4: Nodes gradually disappear (transparency increases)
- Keyframes 4–5: Nodes are fully transparent again
This type of transition is particularly useful when you want to:
- Draw attention sequentially to multiple regions or molecules
- Highlight how a ligand docks into a binding pocket
- Temporarily hide contextual information and bring it back later
How to Apply Pulse
Start by selecting the nodes you want to animate—be it visual models, structural components, or labels. Then, in the Animation panel of the Animator, double-click on Pulse.
The animation is automatically applied with default keyframes. You can drag these keyframes along the timeline to adjust the timing of the animation to suit your presentation rhythm or to synchronize it with other animated events.
Fine-Tuning Transitions
By default, the transparency changes apply uniformly between keyframes, but you can go further. SAMSON allows you to edit the Easing curve, giving you control over how fast or slow the transitions feel. For example, you can make nodes fade in quickly but fade out slowly—ideal for simulating the pulsing behavior of biological systems (hence the name).
Use Cases
The Pulse animation is a simple but versatile tool. Here are a few ways molecular modelers are using it:
- Cycle highlights: Use Pulse to loop attention between different conformations or binding modes.
- Layer visibility: Temporarily reveal annotations or surrounding structures.
- Focus transitions: Guide the viewer’s eye as you move between different molecules or complexes.
For molecular modelers frequently asked to communicate results visually—whether during research presentations, collaborations, or video productions—the Pulse animation offers a flexible way to add visual rhythm and clarity to your scenes.
To learn more and see additional examples, visit the official documentation page for the Pulse animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.