One common challenge in molecular modeling and presentation is managing visual clarity when dealing with complex systems. It’s easy for key elements to get lost in a mess of atoms and bonds, especially in animated sequences where the molecular structure changes over time. Fortunately, in SAMSON, you can temporarily hide parts of your model during animations without deleting or altering your data. This allows you to direct focus exactly where it’s needed — and bring elements back into view at precisely the right moment.
This blog post explores the Hidden animation tool in SAMSON and how it can help molecular modelers create clearer, more effective animations. We’ll look at when and how to apply it, and how it differs from similar animation effects like Hide and Disappear.
Why Use “Hidden” Instead of Changing Transparency?
There are multiple ways to reduce visual clutter in molecular presentations — using transparency is one often-used approach. However, transparency still displays part of the structure, which can be distracting, especially in dense views. The Hidden animation in SAMSON is more decisive: it toggles the visibility of nodes between two keyframes instead of just making them semi-transparent. Hidden nodes are completely invisible, enabling a cleaner viewport and better focus for your audience.
How It Works
The Hidden animation is applied through the Animator module in SAMSON. Here’s how to use it effectively:
- Select the nodes (e.g., atoms, bonds, molecular groups) you want to hide during part of the animation.
- In the Animation panel of the Animator, double-click on the Hidden animation. This sets the starting keyframe at the current frame.
- Drag or adjust the end keyframe to match the desired duration of your hidden animation phase.
- You can move the keyframes around any time to change the timing of visibility transitions.
This creates an interval where the selected nodes completely disappear from view — and then reappear again when needed. Unlike with some other effects, you don’t have to dial in opacity levels or worry about layering issues: they’re simply not shown at all.
A Visual Example
Below is an example animation where different parts of a molecular system are alternately shown and hidden to enhance focus:
In this animation, you can clearly see how sections of the structure vanish entirely, allowing attention to shift to what’s still visible. Later, they return smoothly. This approach is especially useful during step-wise mechanism demonstrations or time-lapse conformational changes.
Control Over Transitions: Easing Curves
SAMSON also gives you control over how transitions occur via Easing curves. This lets you fine-tune how smoothly your Hide-reveal cycles behave over time. Whether you want the nodes to pop in/out suddenly or fade gradually (still fully disappearing between frames), easing options let you adjust keyframe dynamics.
When to Use Hidden
Use the Hidden animation when:
- You want to temporarily remove visual distractions (e.g., solvent molecules).
- You are layering multiple structures in a single animation and want to alternate focus.
- You need to prepare clear, pedagogical animations for courses or presentations.
Just remember: this effect deals with visibility, not rendering settings. It’s a simple but powerful feature to make animations more viewer-friendly.
To learn more and integrate the Hidden animation into your workflows, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/hidden/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.