When visualizing complex molecular systems, clarity is essential. Often, parts of a structure temporarily obstruct your view of regions of interest, such as an active site or a particular interaction interface. While hiding parts of the model solves this problem, it often feels abrupt and visually jarring. Enter progressive transparency.
In SAMSON, the Disappear animation allows molecular modelers to make nodes gradually fade away, rather than disappear instantly. This subtle effect can improve clarity in presentations and research visuals without breaking the viewer’s sense of continuity.
Why fading is better than hiding
The Hide animation in SAMSON removes nodes from view instantly. However, this kind of sharp transition sometimes makes it hard to follow the context of what’s being removed—especially in dynamic visualizations like movies or interactive presentations.
The Disappear animation solves this problem by introducing progressive transparency. By gradually increasing the transparency of selected nodes, you allow audiences to visually track components as they fade out. This smoother visual cue is easier to follow, looks more natural, and maintains spatial relationships during transitions.
How it works
To use the Disappear animation:
- Select the nodes in your scene that you wish to fade out. These must support transparency. This includes structural models, visual models, meshes, and labels.
- Open the Animator and double-click on the Disappear effect in the Animation panel.
- Adjust the keyframes: the animation uses four of them by default.
- Between keyframes 1 and 2: nodes are fully opaque.
- Between keyframes 2 and 3: nodes become gradually transparent.
- Between keyframes 3 and 4: nodes are fully transparent.
This staged transition allows you to control exactly when and how fast nodes fade, and you can shift the keyframes to align with other animations or presentation timing.
Common use cases
Modelers frequently use Disappear animation for:
- Exposing deep regions of biomolecules by progressively fading the outer parts of a protein shell.
- Creating clean visual narratives where different structural domains fade one after another to focus attention.
- Teaching and communication, where a gradual fade-out desaturates visual clutter without teleporting atoms out of view.
Limitations to keep in mind
Individual atoms and bonds don’t have adjustable transparency in SAMSON. To change their apparent opacity, you’ll need to apply the animation to their containing structural models.
Also, if nodes don’t support the transparency attribute, the Disappear animation behaves like the Hide animation instead—instant removal.
Tips for smoother transitions
If you’re integrating Disappear into longer animations, consider changing the Easing curve to fine-tune the speed of fading. This adds another layer of control and can make your animations even more seamless.
For demos and visuals that feel more polished and intelligible, Disappear is a tool worth incorporating into your workflow.
Learn more about the Disappear animation 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.