When telling the story of a complex molecular system, timing and visual consistency can have a significant impact on comprehension. Many researchers and educators rely on animations to construct engaging molecular presentations. However, a common challenge arises when trying to gently remove elements from the scene.
The basic Hide and Show animations in SAMSON completely remove or reveal elements between keyframes, often resulting in abrupt transitions. If your goal is to smoothly fade parts of a molecular model to focus attention or suggest a temporal or spatial progression, the Disappear animation can be a more effective option.
What is the Disappear Animation?
The Disappear animation gradually increases the transparency of selected nodes in your molecular scene until they become fully invisible. It’s particularly useful for highlighting a subregion of interest by fading out surrounding elements, or for simulating progressive transformations, like ligand release or molecular assembly.
It can be applied to any nodes that support the transparency attribute, such as:
- Structural models
- Visual models
- Meshes
- Labels
Note that individual atoms and bonds do not have transparency themselves. Instead, apply the animation to their parent structural model to control their opacity.
Controlling the Fade Sequence
The Disappear animation includes four keyframes for accurate control:
- Keyframes 1–2: Nodes remain fully visible (opaque)
- Keyframes 2–3: Transparency increases gradually
- Keyframes 3–4: Nodes become fully transparent
This gives you control over both when the fade starts and how long it lasts.
You can reposition these keyframes to match the narrative pace of your presentation. Quick transitions can draw focus suddenly, while slow fades support more meditative explanations.
Fine-Tuning the Visual Flow
By editing the Easing curve of the animation, you can customize how the transition behaves between keyframes. For example, a curve that starts slowly and accelerates gives the impression of an emerging discovery, while a deceleration creates a sense of fading memory or dissolution.
This control makes it easier to match visual flow with narrative tone—key when explaining complex phenomena like protein folding, binding pathways, or data provenance.
When to Use Disappear Instead of Hide
Choose Disappear when:
- You want to gracefully transition out parts of a system
- You aim to retain spatial continuity as parts of the molecule fade
- You are building illustrative or cinematic scientific presentations
In contrast, Hide simply snaps items off the canvas—with no transparency steps in between.
To add the Disappear effect in SAMSON:
- Select the nodes you want to fade.
- Double-click the Disappear animation in the Animation panel.
- Adjust the keyframes to control timing.
You can learn more about using this animation and its properties on 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 download SAMSON at https://www.samson-connect.net.