Communicating molecular models effectively often comes down to timing. Whether you’re presenting protein-ligand interactions or simulating molecular dynamics, a well-timed pause in your animation can direct your audience’s attention right where it needs to be. In SAMSON, the Pause animation offers a simple way to freeze a frame and allow viewers to absorb its content.
Why is this important? If you’re showcasing something critical — like a molecule docking into a binding pocket, or an intermediate step in a chemical reaction — breezing past the moment in a continuous animation may leave your audience confused or miss the point altogether.
What is the Pause Animation?
The Pause animation in SAMSON lets you stop the flow of movement in your presentation at a given keyframe for a specified duration. Unlike simply stopping the animation, Pause allows your animation to continue afterward, adding rhythm and emphasis to molecular stories.
When Should You Use It?
- Highlighting key conformations: Pause at the exact moment a molecule reaches an important configuration.
- Directing attention: Use a pause before or after a significant transformation or binding event.
- Giving context: Let the viewer orient themselves at the start of the animation before motion begins.
How to Add a Pause
To add a pause in your presentation:
- Open the Animator workspace and locate the Animation panel.
- Double-click the Pause effect to add it at the current frame.
- Use the timeline to move this keyframe to the desired moment in your animation.
Tip
Keyframes can be freely moved along the timeline, giving you full control over where the pause occurs.
Setting the Duration
To specify how long the pause should last:
- Select the pause animation node in the Document view.
- Open the Inspector to reveal the duration setting.
- Enter the desired number of seconds — for example, 3.0 to pause for three seconds.
This level of control allows you to tailor the viewer’s experience by managing the tempo of your molecular narrative.
Example: Pausing for Emphasis
Consider a case where you are demonstrating the docking of a small molecule into its receptor. By adding a pause just as the molecule aligns perfectly in the binding site, you give your audience a moment to interpret the arrangement of hydrogen bonds or hydrophobic interactions before the animation continues.
Final Thoughts
The Pause animation may seem like a small tool, but it can have a big impact on how effectively you communicate your molecular models. It’s perfect for educational content, scientific talks, or any molecular visual story where clarity and pacing matter.
To learn more about the Pause animation, you can visit the full documentation page here: documentation.samson-connect.net/users/latest/animations/pause/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.