When working on complex molecular systems, it’s easy to feel overwhelmed by the sheer number of elements in the scene. Whether you’re visualizing protein interfaces, understanding conformational changes, or creating compelling molecular presentations, sometimes the challenge is simply guiding the viewer’s eye.
That’s where the Pulse animation in SAMSON can make a difference. Unlike static visualizations, Pulse adds dynamic flow, helping you emphasize structural elements by making them gracefully appear and disappear. This technique is particularly helpful for educators, researchers creating presentations, or anyone preparing molecular animations for a broader audience.
What does Pulse actually do?
The Pulse animation in SAMSON gradually increases and then decreases a node’s opacity, essentially making parts of your model gently fade in and out. It’s a visually effective way to highlight structures without permanently hiding or isolating them.
This animation works with any node that has a transparency attribute, including:
- Structural models
- Visual models
- Meshes
- Labels
Pulse follows this 5-keyframe principle:
- Keyframes 1–2: Node fully transparent
- Keyframes 2–3: Node gradually fades in
- Keyframe 3: Node fully visible
- Keyframes 3–4: Node gradually fades out
- Keyframes 4–5: Node fully transparent again
This ‘breathing’ effect not only adds visual interest, but also functions as a temporal spotlight, subtly directing attention to elements as they come and go from view.
When is Pulse most helpful?
Pulse is particularly useful when:
- You want to draw attention to a part of the model without isolating it
- Explaining cyclical or periodic processes, like heartbeat-related protein activity or gating of ion channels
- You’re building an animation and need a smooth, non-distracting way to show elements sequentially
It’s a minimal intervention that speaks clearly.
How to apply Pulse
To set it up, follow these steps:
- Select the desired nodes in your scene.
- Open the Animation panel in the Animator.
- Double-click on the Pulse animation effect.
- Adjust the keyframes to match the timing you need. For example, make Pulse slower for calming emphasis, or faster for alerting sequences.
You can further refine the motion by adjusting the easing curve, which changes how the transparency interpolates between keyframes—linear, ease-in, ease-out, or custom.
Preview: What it looks like
The example above illustrates the full Pulse cycle. You can imagine using this to guide the focus toward a specific ligand binding site or highlight a label in a periodic manner to emphasize a key residue.
Why not just use ‘Appear’ or ‘Hide’?
While instructions like Appear or Hide are abrupt and binary, Pulse enables a softer transition where molecular components gently come into view and then fade out. This difference in pacing and subtlety can be crucial when producing visuals intended to teach or present complex biomolecular data.
Explore More
The Pulse animation can be the quiet workhorse in your animation toolkit—very effective when used thoughtfully.
To dive deeper or experiment with it directly, check out the original documentation page on Pulse: https://documentation.samson-connect.net/users/latest/animations/pulse/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON from https://www.samson-connect.net