Communicating molecular mechanisms can be challenging—small differences in conformation or key structural steps are often lost in movement-heavy animations when every detail overlaps. For molecular modelers preparing presentations, teaching materials, or publication visuals, the ability to emphasize when a group of atoms or molecules appear or disappear can make all the difference in clarity.
This is where SAMSON’s Flash animation effect can be particularly helpful. Instead of fading molecules in and out through transparency (which can sometimes dilute contrast with a busy background), Flash controls visibility directly: the nodes you choose are either visible or not, with precise control via keyframes.
What does ‘Flash’ do?
In SAMSON, a node typically refers to anything in your document: a molecule, a part of a molecule, a selection of atoms, etc. When you apply the Flash animation to nodes, you define when they are visible, using four keyframes:
- Keyframes 1 → 2: the nodes are hidden
- At Keyframe 2: the nodes suddenly appear
- Keyframes 2 → 3: the nodes are visible
- At Keyframe 3: the nodes disappear again
- Keyframes 3 → 4: the nodes remain hidden
This approach allows clear emphasis on “step-like” transitions in molecular processes. For example, if you’re modeling a ligand binding event, Flash could be used to show the moment of ligand appearance inside a binding pocket, followed by its disappearance to mimic release. No clutter, no gradual fade—just clean transitions that are easy to follow.
How to apply the Flash animation
Here’s how you can use the Flash animation inside the SAMSON platform:
- Select the node(s) you want to animate (e.g., a molecule, a protein subunit, or other visual components).
- Open the Animation panel in the Animator.
- Double-click the Flash effect.
- Adjust the position of the four keyframes to match the timeline of your animation.
You can further refine the timing and dynamics of the appearance/disappearance by editing the Easing curve, which lets you control how quickly these transitions occur relative to the surrounding frames.
Why not just use transparency?
While transparency effects have their place, they may not always clearly signal the arrival or departure of important molecular entities, particularly in videos with multiple overlapping elements. Flash ensures there’s no ambiguity: viewers clearly see when a structure appears and disappears. This makes it especially useful in:
- Presentations of molecular mechanisms (e.g., extrusion or docking steps)
- Teaching materials where you want to show rapid conformational changes
- Focus shifts in multistep simulations (e.g., enzyme cycles)
At any moment, you can move the keyframes to play with timing and sync your visual highlight with other movements in your scene. It’s a simple yet versatile tool.
To learn more about the Flash animation effect, consult the official documentation here: https://documentation.samson-connect.net/users/latest/animations/flash/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net