Molecular modelers and educators often face the challenge of drawing attention to specific regions of a molecule during presentations or animations. Whether you’re preparing a lecture, a publication figure, or an animation for collaboration, it’s sometimes essential to progressively hide certain atoms or bonds without creating clutter or confusion.
In SAMSON, the Conceal atoms animation effect provides a neat solution to this problem. This feature lets you make atoms (and bonds between them) disappear gradually between animation frames — not by fading them using transparency, but by adjusting their visibility. This results in a cleaner and more intentional visual effect compared to just dialing down the opacity.
How It Works
To use the Conceal atoms animation in SAMSON’s Animator:
- Select the atoms (and bonds) you want to make disappear.
- In the Animation panel of the Animator, double-click on the Conceal atoms effect.
This inserts an animation with four keyframes:
- Keyframe 1 to 2: All chosen atoms and bonds are visible.
- Keyframe 2 to 3: Atoms and bonds gradually disappear. The order depends on your selection.
- Keyframe 3 to 4: All selected atoms and bonds are hidden.
You can drag the keyframes to different moments in your timeline to control the speed and timing of the concealment effect. Additionally, if you need fine-tuned control over how the animation progresses, you can adjust the easing curve to modify how the visibility changes over time.
Why Use It?
This technique can be especially helpful in several scenarios:
- Focusing attention on a reaction site by gradually hiding non-essential parts of the molecule
- Creating before-and-after visualizations in structural studies
- Enhancing clarity in tutorials and lectures by removing complexity in steps
- Making fly-over animations more engaging by hiding regions you’ve already discussed
By using visibility (rather than fading via transparency), the Conceal atoms effect avoids the visual clutter that often results from semi-transparent components overlapping with others.
Real-World Examples
Here are some presentation examples that creatively use the Conceal animation in SAMSON:
- 1AF6 – Fly around — A rotating view of a protein where regions gradually disappear
- 1AF6 – Fly around – 2 — A variation with slightly different pacing and emphasis
Other Animation Options
If you’re interested in similar effects, check out related animation types like Reveal atoms, Appear, or Flash. These different styles can help you add diversity and clarity to more complex animations where static images aren’t enough.
To learn more about how to use the Conceal atoms effect, visit the official documentation page here: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.