One of the challenges faced by many molecular modelers when preparing visualizations is controlling the timing and visibility of molecular components in animations. Whether you’re building an educational video, a research presentation, or simply exploring dynamic behavior, it can be difficult to manage when molecular structures should appear or disappear — especially if you’re relying on manual transparency toggles or combining multiple animation effects to get a simple result.
The ‘Show’ animation in SAMSON offers a cleaner, more efficient solution, particularly when all you want is for selected molecular entities to appear at a specific point in time and remain visible. Instead of juggling consecutive Hidden and Shown effects, ‘Show’ handles this with a single animation block.
What is the ‘Show’ Animation?
The ‘Show’ animation makes selected nodes visible at a specific keyframe. From that point forward, the nodes remain visible until the end of the animation. This visibility toggle is performed without altering transparency settings, keeping things clean and simple.
The main advantage of using ‘Show’ is that it abstracts away the usual two-step process of making something appear by first hiding it and then showing it — which is especially helpful when working with intricate molecular assemblies where timing matters.
When to Use the ‘Show’ Animation Effect
Consider a scenario where you’re presenting a molecular complex and only want specific subunits to appear as the presentation progresses. Instead of manually adjusting the transparency and visibility frame by frame, you can:
- Select the component nodes you wish to reveal.
- Double-click on the ‘Show’ animation in the Animator‘s Animation panel.
- Adjust the three keyframes to match your timing:
- Keyframes 1–2: component is hidden.
- At Keyframe 2: component appears.
- Keyframes 2–3: component remains visible.
This solves a common pain for modelers preparing sequences where new parts of a molecule should be introduced progressively — for instance, during a ligand docking simulation, subdomain assembly, or a reaction pathway visualization.
Tips for a Smooth Workflow
- Leverage the Timeline: Move and adjust keyframes as needed to fine-tune visibility transitions.
- Use Easing Curves: Modify interpolation styles between frames to create smoother animations. This is useful even if you’re only toggling visibility since it may enhance the perception of timing and flow.
- Stay Organized: Naming and grouping your nodes helps keep animations manageable when working with complex systems.
While the original documentation references an outdated menu system, all animations are now available through the Animation panel in SAMSON’s Animator. As of the current version, this is accessible via the interface or using shortcut Ctrl+7 (or Cmd+7 on macOS).
By simplifying a historically clunky process, the ‘Show’ animation provides a more intuitive way to control the narrative of your molecular visualizations. Whether you’re preparing educational content or documentation for collaboration, a well-timed appearance can go a long way in making your story clearer.
To explore additional animation effects like Appear, Disappear, or Flash, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.