Visualizing complex molecular models often involves toggling visibility—switching parts on and off to focus attention or guide a viewer through a process. But a sudden change from invisible to visible can break immersion in animations or video presentations. This is a common issue, especially in structural biology, materials science, or drug design demonstrators. A smoother alternative is to make models gently appear, creating a more natural and visually pleasing transition. SAMSON offers a way to do this using the Appear animation.
The Appear animation is designed specifically for nodes that support transparency. This includes structural models, visual models, meshes, and labels. The idea is simple: rather than suddenly showing something, let it progressively become visible by decreasing its transparency over time.
Where This Matters
In presentations or instructional videos, progressive appearance can help you:
- Direct viewer focus to a new structural element
- Layer complex molecular assemblies gradually
- Create smoother animations for publication or teaching
However, not all model elements support this kind of animation. Individual atoms or bonds don’t have a transparency attribute. Their parent structural models do. This means you’ll want to apply the Appear animation at the structural model level, not to individual atoms.
How It Works
After selecting your nodes, apply the Appear animation by double-clicking it in the Animation panel of the Animator. You’ll get an animation sequence with four keyframes:
- Keyframes 1 to 2: Object stays fully transparent
- Keyframes 2 to 3: Transparency decreases, object gradually appears
- Keyframes 3 to 4: Object remains fully visible (opaque)
These points are designed to give you control over when the object starts appearing and how long it takes. You can move keyframes freely to fine-tune this timing.
Controlling the Transition Curve
You can also modify how the transparency changes over time (e.g., accelerating or decelerating) by editing the Easing curve. This is useful for producing more natural-looking animations—like a slow fade-in versus a linear reveal.
Visual Example
The animation below shows how structural elements can gently appear and disappear using behavioral transparency.
Other Things to Keep In Mind
This animation complements others like Show, which instantly makes an object visible. For nodes that don’t support transparency, Show will produce a similar result—but without the fade-in effect.
For complex sequences, the Appear effect can be combined with others like Flash or Pulse. Start with Appear, then follow with more dynamic effects to guide the audience through structural features.
To learn more and see all animation options, visit the documentation page for the Appear animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.