One of the challenges molecular modelers often face when creating scientific presentations or molecular animations is the need to gradually hide parts of their models—without having them abruptly vanish. Whether preparing educational content, highlighting results in a collaborative setting, or crafting compelling visualizations for research outputs, smooth transitions are key to keeping viewers engaged and well-oriented.
That’s where the Disappear animation in SAMSON can help. Rather than instantly hiding nodes—an interaction that can feel jarring or even disorienting—the Disappear animation makes parts of your molecular scene progressively fade out. This is especially helpful when you want to guide your audience’s attention smoothly from one region of a complex model to another.
When to Use the Disappear Animation
The Disappear animation is suitable for structural models, visual models, meshes, and labels—anything with a transparency attribute. If you’re working at the atom or bond level, apply the animation at the structural model level, since individual atoms and bonds do not have their own opacity settings.
How It Works
To apply the Disappear animation in SAMSON:
- Select the nodes you want to fade out.
- Open the Animation panel from the Animator.
- Double-click on the Disappear effect.
This adds a timeline with four keyframes:
- Keyframes 1 to 2: Nodes remain fully visible (opaque).
- Keyframes 2 to 3: Transparency increases—this is where the fade-out occurs.
- Keyframes 3 to 4: Nodes are fully invisible (transparent).
You can reposition the keyframes freely to control the timing and duration of each stage. For even more customization, use an easing curve to control how the transparency changes over time—for instance, starting slowly and then fading out more quickly.
A Real Example
In the example below, a structure smoothly fades out using the Disappear and Appear effects in sequence. This technique can be valuable for visual storytelling: molecules can appear, transform, and disappear to highlight specific mechanisms or conformational changes.
Final Tips
- Don’t forget that this animation affects only nodes with opacity settings. If you don’t see the effect, check whether your selection supports transparency.
- The Disappear effect is non-destructive—you’re not deleting parts of the model, just changing their visibility.
- Use it in combination with the Appear animation for toggling structures on and off gracefully.
To explore more about how to use this and other animation tools in SAMSON, visit the full documentation page on Disappear animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.