When preparing animations for scientific presentations or teaching materials, molecular modelers often face a common challenge: how to clearly show the removal or disappearance of molecular parts without making the transition feel abrupt. Using simple hide/show toggles can break the narrative flow and make it harder for viewers to follow what happened. This is where a smooth transparency-based animation—rather than a sudden hide—can make a real difference.
In SAMSON, the Disappear animation addresses this need by gradually increasing the transparency of selected molecular models or annotations. Whether you’re working with structural models, visual elements like meshes, or labels, the Disappear animation helps you communicate molecular events or focus shifts with clarity and visual elegance.
What Disappear Does
The Disappear animation in SAMSON makes nodes that support transparency progressively vanish. This differs from the basic Hide animation, which simply toggles visibility off. Disappear, on the other hand, creates an interpolation of transparency values that adds continuity to your animation scenes.
This animation works on:
- Structural models (such as whole molecules)
- Visual models (e.g., surfaces)
- Meshes
- Labels
Important note: individual atoms and bonds themselves don’t support opacity directly. To make them disappear, apply the animation to the structural model that contains them—not to the atoms or bonds separately.
How the Animation Works
The Disappear animation uses four keyframes:
- Between keyframes 1 and 2: the object remains fully visible (opaque).
- Between keyframes 2 and 3: transparency increases gradually.
- Between keyframes 3 and 4: the object is fully transparent (effectively invisible).
You can freely move the keyframes along the timeline to control how quickly or slowly the disappearance occurs.
Tip: For subtle effects, place keyframes 2 and 3 further apart. For a quick fade-out, bring them closer together.
Creating a Disappearance Effect
- First, select the nodes you wish to animate.
- Open the Animation panel in the Animator interface.
- Double-click the Disappear animation.
- Adjust the keyframes as needed.
An easing curve setting allows you to fine-tune how transparency changes over time—linear, ease-in, ease-out, or custom curves supported in SAMSON’s animator timeline.
Example: Appear and Disappear Combined
Below is a visual example combining the Appear and Disappear animations, showing how molecular components can smoothly come into view and then fade out. This kind of animation can be useful when simulating dynamic events like ligand binding, unfolding, or molecular drilling.
Use Cases in Molecular Modeling
The Disappear animation is helpful in many scenarios:
- Showing sequential assembly or disassembly of molecular complexes
- Highlighting structural changes by clearing away parts of the model
- Steering attention to selected components by fading background elements
- Creating engaging visualizations for publications and lectures
You can learn more here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.