Visualizing molecular systems over time is a key aspect of effective scientific communication, especially when building presentations or educational material. One frequent need among molecular modelers is to illustrate the gradual disappearance of parts of a system—say, to focus attention on a reaction site or reveal underlying structural elements.
If you’ve ever wanted to make your molecules gradually fade from view rather than instantly hiding them, the Disappear animation in SAMSON provides a straightforward and intuitive approach for that.
Why Use Disappearance Over Instant Hiding?
Using transparency instead of simply turning off visibility can offer a more fluid and pedagogical experience. Instead of snapping elements out of existence, you can:
- Direct viewer attention smoothly
- Clarify spatial hierarchies
- Maintain context as parts of a system gradually vanish
What Can Be Made Transparent?
The Disappear animation only works on nodes with a transparency attribute. These include:
- Structural models
- Visual models
- Meshes
- Labels
It’s important to note that atoms and bonds alone do not have an opacity attribute, but their parent structural models do. If you want atoms and bonds to vanish progressively, you must animate the structural models that contain them.
How to Set It Up
Adding the Disappear animation is easy:
- Select the nodes you want to fade out
- Double-click on the Disappear effect in the Animation panel within the Animator
This will automatically create an animation with four keyframes:
- Between frames 1 and 2: full opacity is maintained
- Between frames 2 and 3: transparency increases—nodes fade
- Between frames 3 and 4: nodes are fully transparent
You can adjust the timing between keyframes to match your needs, creating slow fades or abrupt vanishings as needed. You can further control the visual pace by editing the easing curve.
Visual Example
Here is how a combination of the Appear and Disappear animations looks in SAMSON:
A Tip on Compatibility
Some older tutorials and movies might reference the “Animation menu,” which is no longer used in the latest version of SAMSON. All animation effects are now accessible through the Animation panel in the Animator. You can open it via Ctrl+7 (or Cmd+7 on macOS).
Conclusion
The Disappear animation offers molecular modelers an effective way to gently remove structures from view, making it easier to highlight mechanisms, compare conformations, or create captivating molecular movies. Whether you’re explaining enzyme functions or training new scientists, this technique adds an elegant visual layer to your storytelling toolbox.
To learn more, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/disappear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.