When presenting molecular systems to colleagues or students, clarity matters. You want to walk them through a complex structure without clutter, and focus their attention on specific regions. But abruptly hiding parts of a structure can be visually jarring—especially in molecular animations. That’s where animated fading comes in.
The Disappear animation in SAMSON allows molecular modelers to progressively remove structures from view by increasing their transparency. This subtle visual effect feels much smoother than simple hiding, helping you maintain a clean storyline while transitioning between scenes.
Why fade instead of hide?
Imagine showing a protein-ligand interaction. You first display the full protein, then wish to isolate just the active site. Instantly hiding the rest of the molecule can feel like a jump cut. Fading, on the other hand, naturally draws the focus inward, keeps viewers oriented, and makes the transition almost cinematic.
What can disappear?
The Disappear animation targets nodes that support transparency, including:
- Structural models
- Visual models
- Meshes
- Labels
Note: Atomic elements like individual atoms or bonds don’t have transparency attributes—but their structural models do. So if you want the atoms or bonds to fade, apply the animation to their parent structural model.
How does it work?
To use the Disappear animation:
- Select the nodes you want to fade.
- In the Animation panel of the Animator, double-click on Disappear.
The animation uses four keyframes:
- Keyframes 1 to 2: Nodes remain fully opaque.
- Keyframes 2 to 3: Transparency increases gradually.
- Keyframes 3 to 4: Nodes are fully transparent.
You can freely reposition these keyframes to control when and how fast the fading happens, giving you full control.
Fine-tuning the feel
If you want to customize the pacing or feel of the fade, adjust the Easing curve. For example, an ease-in-out curve makes the fade start and end slowly, giving it a more organic feel.
Before you go
Note that the image above shows the legacy Animation menu. In the latest SAMSON versions, all animations are accessed via the Animation panel within the Animator.
Using fade effects thoughtfully can increase the effectiveness of your molecular presentations. Try integrating the Disappear animation into your next sequence to create more intuitive and visually smooth experiences.
To dive deeper into the specifics, check out the full documentation here: https://documentation.samson-connect.net/users/latest/animations/disappear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.