Science communication and molecular modeling often meet at the intersection of clarity and visual storytelling. If you’ve ever prepared an animation to present a molecular assembly or a binding process, you may have faced the challenge of drawing attention to specific structures without overwhelming your audience. Elements that abruptly “pop” into visibility can break the narrative flow, especially when presenting complex systems.
This is where the Appear animation in SAMSON can be helpful. Rather than instantly showing a structure, the Appear effect gradually decreases its transparency, allowing it to fade in smoothly. This subtle difference is useful when guiding a viewer’s attention step by step, for example, when visualizing hierarchical assemblies, conformational transitions, or environments like membranes surrounding a protein.
When to Use the Appear Animation
Use the Appear animation when you want a model or label to fade in gradually, especially in educational videos or presentations. It is particularly helpful for:
- Introducing large macromolecular structures progressively
- Revealing surrounding environments (e.g., lipid bilayers or solvent cages)
- Highlighting newly docked ligands
However, note that only nodes with a transparency attribute – such as structural models, visual models, meshes, and labels – can use this effect. Atoms and bonds do not have a transparency attribute, so apply the animation to the parent structural model instead.
How Appear Works
Once applied via the Animation panel in the SAMSON Animator, the Appear animation uses four keyframes:
- Keyframes 1–2: Nodes are fully transparent
- Keyframes 2–3: Nodes progressively fade in
- Keyframes 3–4: Nodes are fully opaque
This structure is flexible: you can move the keyframes to control exactly when the nodes start and finish appearing.
The easing curve between the keyframes can also be adjusted. For example, a slow-start fast-end transition can make elements appear more naturally.
Practical Tip: Focus Your Viewer
When presenting a ligand binding into a pocket, consider the following technique:
- Show the protein structure alone for a few seconds
- Use the Appear animation to gradually reveal the ligand
- Optionally, fade in surrounding solvent molecules afterward
This way, the viewer’s attention starts on the target structure before progressively introducing the ligand and its environment. The animation mirrors the process you’re discussing, reinforcing understanding.
Updated Interface Note
Earlier versions of SAMSON included an Animation menu, but this has now been replaced by the Animation panel inside the Animator. You can launch it using:
- Ctrl + 7 on Windows/Linux
- Cmd + 7 on macOS
Visual Example
Here is an example from the documentation showing a fade-in/fade-out sequence of molecular components using the Appear (and Disappear) animations:
Combining clear visuals and thoughtful animation pacing can make a big difference in your storytelling, especially for diverse audiences ranging from research collaborators to students.
To learn more, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.