When creating animations of molecular systems, visual clarity is important not just for aesthetics, but also for scientific communication. One common issue faced by many modelers is the abrupt appearance of structures between frames, especially when transitioning between different stages of a reaction or conformational change.
Instead of relying on transparency effects, which may create rendering inconsistencies or visual ambiguity, it is often more effective to animate visibility directly.
Smooth visual transitions using the “Shown” animation
In SAMSON, the Shown animation is a dedicated effect that lets you explicitly control whether nodes (atoms, residues, structures, etc.) are shown in a certain time interval during an animation. This level of control is especially useful when you are:
- Gradually building up a system for a presentation
- Highlighting key components only at specific frames
- Creating clear before/after comparative sequences
Unlike opacity-based transitions that sketch objects in semi-transparent layers (which might confuse viewers), the Shown animation hides nodes completely outside keyframes, making your message clearer.
Adding a Shown animation step-by-step
- In your SAMSON workspace, select the nodes you want to reveal during your animation.
- Go to the Animation panel inside the Animator.
- Double-click on the Shown animation effect. A new animation block will be created, with its beginning keyframe placed at the current frame.
- You can then move or adjust keyframes in the timeline to fine-tune when the nodes appear or disappear within your animation.
Shown animations, when combined with other visibility-related effects such as Hidden, Appear, or Pulse, open up creative ways to tell precise stories using molecular systems. You might use Shown to gradually build up a protein’s active site while pulsing the ligand to highlight binding.
Customizing transitions
While the Shown effect is binary (a node is either visible or not), you can fine-tune how it integrates into your broader animation by adjusting the timing and positioning of its keyframes. To control the pace of appearance, you can tweak the easing curve that determines how animation parameters interpolate between frames. This becomes relevant especially when choreographing Shown animations alongside movement or color changes, allowing for synchronized transitions.
By combining visibility control with movement and highlighting effects, you can guide your audience’s attention and avoid visual overload. This is particularly helpful when preparing instructional videos, academic presentations, or publication supplements.
To learn more: documentation.samson-connect.net/users/latest/animations/shown
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.