Molecular modeling often involves complex, dynamic simulations where every second counts — literally. When giving a molecular presentation or preparing an animation of a simulation, highlighting specific structural changes at the exact moment they occur can greatly enhance understanding. But what if you need your audience to have just a little more time to absorb what’s being shown before moving on to the next frame?
This is where the Pause animation in SAMSON becomes incredibly useful. It allows modelers to pause a molecular animation at any keyframe for a specific number of seconds, making sure viewers have the chance to fully analyze what’s being presented — without manually editing the animation or video.
Why a Pause Can Make All the Difference
Imagine you’ve created an animation of a docking pathway between a ligand and its receptor. As the ligand approaches the binding site, you want to call attention to a conformational change in one of the side chains. If the animation plays at normal frame rate, this important detail might be missed by viewers.
With the Pause effect, you can hold the animation exactly at that key point for, say, 3 or 4 seconds. This gives your audience enough time to notice the rearrangement, reflect on what it means, and be fully oriented for what comes next.
How to Add a Pause in SAMSON
Adding the pause is straightforward:
- Open the Animation panel.
- Double-click on the Pause effect. This adds a keyframe at the current frame.
- Drag the keyframe to the precise moment you want to pause, if needed.
Tip: Keyframes are always movable, so you can fine-tune their timing to match critical events in your animation.
Setting the Duration
Once the pause is placed, you can customize its duration through the Inspector:
- Select the pause animation node from the Document view.
- The Inspector will show the properties of the pause effect. Enter your desired duration in seconds.
This setup lets you control the narrative rhythm of your presentation. You’re not bound by the simulation’s internal time steps; instead, you can match the flow of your explanation to your audience’s pace of comprehension.
When to Use It
Some great uses for adding pauses include:
- Highlighting the emergence of a hydrogen bond.
- Pausing at reaction intermediates during a catalytic cycle.
- Marking key moments in docking or unbinding pathways.
- Giving time to discuss something live during a conference presentation or video narration.
When used thoughtfully, a pause can transform a passive animation into a compelling scientific story.
To learn more and view the full documentation, visit the original page here: https://documentation.samson-connect.net/users/latest/animations/pause/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.