A common challenge in molecular modeling is effectively communicating complex 3D structures and dynamic behaviors to both colleagues and broader audiences. Whether for presentations, publications, or teaching, clarity and visual engagement are key – and this is where animations shine.
Among the available animation effects in SAMSON, the Pulse animation provides a simple yet powerful way to draw attention to specific structural elements. It creates a “breathing” effect by making selected objects fade in and out cyclically, which can help viewers understand which regions are dynamic, functionally important, or temporally variable.
What is the Pulse Animation?
The Pulse animation works by manipulating the transparency of selected nodes. These nodes can be:
- Structural models
- Visual models
- Meshes
- Labels
The key idea is that elements progressively appear and disappear during the animation cycle. The supporting timeline is made of five keyframes:
- Full transparency
- Still fully transparent
- Fully opaque
- Becoming transparent
- Back to full transparency
Visually, this results in a pulsating effect — hence the name. Despite its simplicity, this effect is particularly suited to highlight default-invisible components, guide a viewer’s eye, or create rhythms when combining multiple animations in a scene.
How to Add the Pulse Animation
To use the Pulse animation in SAMSON:
- Select the nodes you’d like to animate (e.g., a ligand binding site or a highlighted surface).
- Go to the Animation panel within the Animator.
- Double-click on the Pulse effect.
Once applied, you will see five keyframes. You can move these keyframes along the timeline to change the speed and timing. For example, spreading them out creates a slower pulse, while bringing them closer together speeds up the effect.
Customizing Interpolation
The Pulse effect can further be refined using the Easing curve. This controls the interpolation between keyframes and allows, for example, for a slower fade-in and quicker fade-out — providing room for storytelling and attention guidance.
When to Use Pulse
The Pulse animation is ideal in several specific modeling scenarios:
- Highlighting fleeting molecular interactions like hydrogen bonds or allosteric sites.
- Visualizing molecular assemblies by sequentially introducing their parts.
- Teaching molecular processes by creating rhythmic cues to aid memory and clarity.
Combining multiple Pulse animations with different timings and targets can lead to engaging visual workflows. Whether you’re creating lecture material or studies for peer review, using this effect strategically can make your work more interpretable.
To learn more, 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.