Communicating molecular insights often requires more than just static images. When presenting dynamic processes like conformational changes, reaction mechanisms, or structural rearrangements, fine control over visibility can convey meaning more effectively. A common issue for molecular modelers is how to transition complex structures out of view in an elegant, clear way—without jarring visual interruptions or sudden content removal.
This is where the Disappear animation in SAMSON can be quite useful. Unlike simple hiding tools, the Disappear animation allows nodes to progressively fade out based on their transparency attribute, enabling scientists and educators to stage visual narratives that smoothly guide attention and emphasize key transformations.
Why It Matters
Imagine displaying a protein interacting with a ligand, and then needing to focus the viewer’s attention solely on the binding site. The abrupt disappearance of surrounding atoms might feel disorienting. A gradual disappearance, however, helps ease the transition, preserving spatial context and enhancing visual clarity.
With the Disappear animation in SAMSON, modelers and presenters can:
- Control timing and smoothness of transparency transitions
- Coherently fade out full structural or visual models, groups, meshes, and even labels
- Clarify visual focus without removing spatial or temporal continuity
How It Works
The Disappear animation applies only to nodes that support transparency—primarily structural models, visual models, meshes, and labels. Individual atoms and bonds, which do not have their own transparency attribute, must be manipulated via their parent structural models.
To use it:
- Select the desired nodes (e.g., a functional domain of a protein).
- Open the Animation panel from the Animator.
- Double-click on the Disappear animation effect.
This animation creates 4 keyframes by default:
- Keyframe 1 to 2: Nodes remain fully opaque.
- Keyframe 2 to 3: Nodes progressively increase transparency.
- Keyframe 3 to 4: Nodes are fully transparent.
You can adjust the keyframes to fit your timing preferences and fine-tune the interpolation using the Easing curve, allowing smoother or sharper fades depending on the effect you need.
Common Use Cases
- Zooming in gently by fading out surrounding models while highlighting a local interaction or active site.
- Layering structural views where portions of a molecule need to successively disappear to expose internal elements.
- Educational storytelling where animations progressively simplify a complex molecular scene for clarity.
If you previously used the Animation menu in SAMSON for this effect, note that it’s now consolidated into the Animation panel in the Animator, which hosts all available animation actions.
This simple but effective visual technique helps molecular modelers avoid abrupt visual shifts and makes presentations or videos more digestible for diverse audiences.
Learn more and view the complete documentation here: https://documentation.samson-connect.net/users/latest/animations/disappear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.