When creating molecular animations, it’s often challenging to make transitions visually intuitive. If you’re showing a model appear and disappear during a presentation or video, a harsh on–off switch can make the experience jarring. This is particularly relevant for molecular modelers who want to communicate complex transitions without overwhelming their audience.
This is where the Pulse animation in SAMSON can be useful. The Pulse animation effect lets you progressively fade molecular elements in and out, adding polish to your presentation while preserving clarity. It’s designed for use with nodes that support transparency—such as structural models, visual models, meshes, and labels.
What does the Pulse animation do?
The Pulse animation applies a smooth fade-in and fade-out cycle to selected nodes over a sequence of five keyframes:
- Keyframes 1 → 2: Nodes are fully transparent
- Keyframes 2 → 3: Transparency decreases, nodes become visible
- Keyframe 3: Nodes are fully opaque
- Keyframes 3 → 4: Transparency increases, nodes begin disappearing
- Keyframes 4 → 5: Nodes are fully transparent again
This loop structure provides an eye-catching, non-disruptive way to draw attention to particular structures in a model, or emphasize transitions between states such as ligand binding or conformational changes.
How to use it
To apply the Pulse effect in SAMSON:
- Select the nodes you wish to animate.
- Open the Animation panel found in the Animator.
- Double-click the Pulse animation to add it to your sequence.
- Customize the placement of keyframes as needed to match the timing of your presentation or simulation.
Customizing the animation
You aren’t limited to linear transitions. In the Inspector, you can modify interpolation by choosing different easing curves. This allows you to create delays at the start or end of pulses, or ease in and out progressively based on the shapes of the curves you select.
Why this is helpful
Progressive transitions like Pulse reduce cognitive load on your viewer. If you’re showing multiple conformations, or highlighting specific subunits, the gradual appearance and disappearance make the whole process easier to follow. It’s particularly useful in teaching, where you’re building intuition rather than just showing final states. Instead of triggering sudden changes, you can guide the viewer’s attention—and let them absorb the change.
Try it in your next presentation
Whether you’re preparing a lecture, building a video for publication, or simply narrating a molecular event for a colleague, the Pulse animation adds continuity and visual rhythm to your communication.
To learn more, please visit the official documentation page 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