Clarity and visual communication are major challenges in molecular modeling. When crafting animations to illustrate complex molecular phenomena—such as binding events, structural adjustments, or phase transitions—it’s common to feel limited by basic visualization tools. Animations can quickly become cluttered or difficult to interpret as different molecular elements blend into each other or change too abruptly. This is where the Pulse animation in the SAMSON platform can help.
The Pulse animation offers a simple and effective way to focus your viewer’s attention by making selected nodes of your molecular model gently appear and disappear. Instead of moving atoms or rotating structures, Pulse uses transparency to ‘breathe’ components in and out of view, helping you highlight key areas or transitions without altering geometry or structure.
Why Use the Pulse Effect?
Imagine you’re preparing a molecular animation for a conference or educational video. You want to underscore a cofactor entering an active site or DNA wrapping around histones. Overlays and labels could clutter the view—and movement could obscure delicate conformational changes. The Pulse effect solves this by:
- Drawing viewer attention smoothly to one or several molecular components
- Creating a rhythmic in-and-out visibility that mimics biological dynamics
- Allowing contextual comparison between the presence and absence of a structure
All without modifying the actual content of the model.
How It Works
To apply the Pulse effect in SAMSON:
- Select the nodes (e.g., meshes, labels, structural or visual models) that support transparency.
- Open the Animation panel from the animator tools.
- Double-click the Pulse animation from the list. This inserts five keyframes:
- Keyframes 1 → 2: Nodes remain fully transparent.
- Keyframes 2 → 3: Gradual appearance by decreasing transparency.
- Keyframe 3: Full opacity reached—nodes are completely visible.
- Keyframes 3 → 4: Gradual disappearance by increasing transparency.
- Keyframes 4 → 5: Full transparency again.
You can drag the keyframes to adjust timing. This flexibility helps synchronize visual emphasis with other animation elements, such as object movement or label display.
Customizing the Pulse Effect
If you’d like to modulate the pace of transparency transitions, you can adjust the Easing curve. The easing curve controls how quickly or slowly transparency changes between frames, and it allows for complex pulsing behaviors—smooth, linear fades, or more pronounced acceleration effects depending on your goal.
This method of visual storytelling is especially useful when teaching or presenting to an audience unfamiliar with the intricacies of molecules. It adds rhythm and focus, without overwhelming viewers with motion or detail.
Example: Pulse in Action
An example of the Pulse animation applied to a molecular model can be seen below:
You can further tweak how long each transparency state lasts by moving keyframes individually. Need the opaque state to linger? Space out keyframes three and four. Want a quick flash instead? Pull them closer together. SAMSON gives you control without overcomplication.
To learn more about the Pulse animation, 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.