When working with complex molecular systems, clarity and focus are often at odds. Molecular modelers frequently face challenges in presenting results in a way that highlights specific parts of the system without overwhelming the viewer. Whether you’re setting up a presentation, designing an educational video, or simply organizing your workspace, being able to control the visibility of different molecular elements is essential.
One common difficulty involves transitioning parts of a molecular model out of view—especially when trying to maintain a smooth and intuitive visual flow. A sudden disappearance can break immersion or distract the viewer. SAMSON offers a practical solution: the Disappear animation, which allows nodes of the model to progressively become transparent.
Why use progressive disappearance?
The goal here isn’t to hide data, but to guide attention. By fading out less relevant nodes instead of abruptly removing them, you can achieve:
- Focus on key molecular regions
- Gradual storytelling in molecular animations
- Better comprehension for educational or training materials
This feature is particularly useful when working with large complexes or when preparing animations where contextual awareness is critical. With Disappear, your visuals stay informative while becoming more digestible for your audience.
How it works
The Disappear animation in SAMSON smoothly increases the transparency of compatible model nodes over time. It can be applied to nodes that support the transparency attribute, such as:
- Structural models
- Visual models
- Meshes
- Labels
Note that individual atoms and bonds do not have their own transparency settings. If you want to control their opacity, apply the animation to their associated structural models instead.
Adding the animation
To apply the Disappear animation:
- Select the nodes you want to make disappear
- Open the Animation panel inside the Animator
- Double-click on the Disappear effect
This animation includes 4 keyframes:
- Frames 1-2: nodes remain fully visible
- Frames 2–3: transparency increases smoothly
- Frames 3–4: nodes become fully transparent
You can move these keyframes to adjust timing and synchronization with other elements of your animation. For even more control, modify the easing curve to change how the transparency progresses over time.
Example use case
Suppose you’re preparing a presentation that illustrates a ligand binding process. Initially, you show the complete protein. Once the binding pocket is introduced, you want to reduce distractions. By applying Disappear to unrelated structural parts, the viewer’s attention is naturally drawn to the critical region as the rest of the protein fades out gradually. It adds one small layer of polish that elevates the explanation.
Learn more about this feature in the original documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.