Whether you’re preparing a presentation or building an educational video, one challenge you may face as a molecular modeler is how to smoothly introduce complex structures. When models instantly ‘pop’ into view, it can feel jarring or overwhelming, especially when showing large biomolecules or assemblies. Using transitional animations not only improves clarity but also helps guide your audience’s attention.
This is where the Appear animation in SAMSON comes in. Rather than instantly displaying nodes (e.g. proteins, meshes, labels), Appear allows you to fade them in progressively based on their transparency. It’s a good way to smoothly introduce parts of a model while building up your scene over time.
What the Appear animation does—and doesn’t do
Appear works well with any node that has a transparency (opacity) attribute. These include:
- Structural models
- Visual models
- Meshes
- Labels
However, individual atoms and bonds do not have a transparency attribute. If you want to animate the visibility of atoms or bonds, apply the Appear animation to their parent structural model instead.
How it works: the four keyframes
Apply the effect by double-clicking on the Appear animation in the Animation Panel after selecting the nodes you want to reveal. This will insert an animation with four keyframes:
- Keyframes 1 – 2: The nodes are fully transparent (invisible).
- Keyframes 2 – 3: The nodes gradually become more visible.
- Keyframes 3 – 4: The nodes are fully visible (opaque).
You can freely move these keyframes to sync the animation with the timing you want. Also, the interpolation between keyframes can be customized using an easing curve, to make the appearance more linear or more organic depending on the mood you’re building.
This can be especially helpful in scenarios like:
- Showing a complex protein step-by-step, starting with domains or chains
- Fading in multiple labels one by one for clarity
- Assembling a molecular mechanism trajectory frame by frame
Planning your animation timing
To avoid overwhelming your audience, consider scattering sequences of Appear animations throughout your presentation or movie. You can combine this effect with others like Disappear or Pulse to highlight what’s most important at each step.
If you’re coming from older versions of SAMSON: note that the Animation menu shown in some older materials is no longer present. Instead, everything is now accessed directly from the Animator’s Animation panel.
If you’re interested in improving the flow of your molecular presentations and making your animations clearer and more engaging, the Appear effect can be a quick and effective tool.
To learn more, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/appear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.