When you’re presenting a molecular system, clarity can make a big difference. Whether you’re teaching, explaining your research, or sharing results with collaborators, the ability to focus viewers’ attention on specific parts of a model is essential. This is where animation becomes a powerful tool—not for aesthetic effects, but for precision and communication.
One common challenge among molecular modelers is how to temporarily highlight certain parts of a structure without clutter, permanent changes, or overuse of labels. If you’re using SAMSON, there’s a subtle—but very useful—animation that can help: Pulse.
What the Pulse Animation Does
The Pulse animation in SAMSON helps molecular elements appear and disappear in a smooth cycle—similar to a blinking effect, but with transparency instead of binary visibility. It works on any node that has the transparency attribute enabled, such as:
- Structural models
- Visual models
- Meshes
- Labels
This makes it ideal for drawing temporary attention to functional groups, ligand binding sites, secondary structure elements, or selected atom groups, while maintaining overall context and visual continuity.
Control Over Keyframes
PULSE works with five keyframes arranged in the following flow:
- Keyframe 1 to 2: Nodes are fully transparent.
- Keyframe 2 to 3: Nodes gradually become opaque.
- Keyframe 3: Full opacity – the nodes are fully visible.
- Keyframe 3 to 4: Nodes fade out to become transparent again.
- Keyframe 4 to 5: They remain fully transparent.
Because you’re in control of these keyframes, you can adjust their positions in the timeline freely. This means you can align the pulsing effect with other events in your animation or synchronize multiple nodes to pulse either together or in wave patterns.
Smooth Transitions with the Easing Curve
One subtle but important feature is the ability to configure the easing curve. This defines how transparency transitions happen between frames—whether they ease in slowly, build quickly, or have custom acceleration. This kind of control lets you tailor the effect for your specific presentation needs, whether it’s subtle emphasis or an attention-grabbing pulse.
How to Add the Pulse Animation in SAMSON
- Select the nodes or elements in your system that you want to highlight (they must support transparency).
- Open the Animation panel in the Animator.
- Double-click on Pulse to apply it to the selected nodes.
- Adjust the timeline keyframes and easing curve as needed.
This simple technique can be especially useful when creating animations for molecular mechanisms, signaling pathways, or structural events where you want part of the system to catch the eye temporarily—without altering the overall view or model structure.
To learn more about the Pulse animation and how it fits into the broader animation toolkit in SAMSON, 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 the platform at https://www.samson-connect.net.