When presenting complex molecular simulations, one of the common challenges is pacing. Animations often move too quickly, not giving viewers enough time to fully observe important transitions, interactions, or structural changes. Whether you’re sharing a ligand binding pathway or a conformational shift, the flow of information needs to match your audience’s ability to interpret it. That’s where the Pause animation in SAMSON becomes an essential tool.
The Pause animation lets you freeze the timeline at a keyframe for a defined number of seconds. It’s simple, but highly effective: instead of rushing through transient molecular events, you create purposeful breathing space. This pause gives your audience — whether they’re students, collaborators, or reviewers — the opportunity to appreciate what just happened right before their eyes.
Why use a Pause animation?
Animations in molecular modeling are often information-dense. A single scene can include multiple structural rearrangements, or a critical interaction forming or vanishing in mere fractions of a second. A well-placed pause allows:
- Clear communication of molecular events
- Improved pedagogical flows for teaching and documentation
- Better impact in scientific presentations
- Intentional pacing for focusing attention
How to insert a Pause
To add a Pause animation in SAMSON:
- Double-click on the Pause effect in the Animation panel of the Animator.
- A keyframe is automatically inserted at your current frame.
- You can move the keyframe to align it with a transition or important moment.
Customization is easy: Once added, simply click on the Pause animation in the Document view and adjust its properties using the Inspector. There you can fine-tune the pause duration, typically specified in seconds.
Whether you want to insert a 1-second pause after a protein docking or a 5-second breathing space before a critical reaction site evolves, this effect gives you control over time without any need for complex scripting.
Pro tip: Stack your effects
Pause animations work especially well when used in combination with other timing tools, like the Stop animation. For example, you can pause to emphasize a structure, then stop the animation altogether to invite questions from a live audience or dive deeper into molecular inspections manually.
Use case: Highlighting ligand binding
Imagine you’re animating a simulation of ligand binding. Right after the ligand enters the active site and forms hydrogen bonds, a short pause of 2 seconds lets your viewers process the geometry of interaction before the animation proceeds into the next step. That brief stillness can make the difference between a viewer missing a key event or clearly understanding it.
If molecular animations are about telling visual stories, then the Pause animation is your punctuation mark. Use it to emphasize and clarify.
To learn more, visit the official documentation on Pause animations in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.