A molecular scene can contain exactly the information you need and still be difficult to read. When several models, meshes, or labels compete for attention, abruptly hiding one may make the transition feel confusing: viewers can lose track of what changed. A gradual fade offers a useful middle ground. It lets you reduce visual emphasis while keeping the presentation’s structure easier to follow.
In SAMSON, the Disappear animation progressively increases the transparency of selected nodes. It is useful when you want to move a presentation from a detailed view to a less crowded one—for example, fading a visual model or label out as attention shifts elsewhere. Think of it as a way to manage visual focus, not as a way to remove molecular content from your document.
Choose the right thing to fade
Start by selecting the nodes that should disappear, then double-click Disappear in the Animation panel of the Animator. The animation can be applied to nodes that have a transparency attribute, such as structural models, visual models, meshes, and labels.
There is an important selection detail to keep in mind: individual atoms and bonds do not have an opacity attribute. Their structural models do. If your goal is to make atoms and bonds appear more transparent, apply the animation to the relevant structural model rather than selecting the atoms or bonds themselves. Otherwise, you may not get the gradual transparency change you intended.
For nodes without a transparency attribute, Disappear behaves similarly to the Hide animation. So before building a presentation around a fade, check that the selected node type supports transparency. This simple check can save time when an animation seems to hide an object instead of gradually fading it.
What the four keyframes do
Disappear has four keyframes, dividing the effect into three stages:
- Between keyframes 1 and 2: the selected nodes remain fully opaque.
- Between keyframes 2 and 3: the nodes progressively disappear as their transparency increases.
- Between keyframes 3 and 4: the nodes remain fully transparent.
This structure gives you a clear way to think about pacing. The first interval provides time in which the object is still fully visible; the middle interval is the actual fade; and the final interval holds the transparent state. You can move the keyframes to adjust when these stages happen in your presentation. If the fade feels too sudden or too drawn out, changing the timing of the keyframes is a practical first adjustment.
Make the transition serve the explanation
Before adding the animation, decide what viewers should notice before and after the fade. If a label is needed to understand the current view, let it remain visible until that explanation is complete. If a model is no longer relevant to the next step, fading it can help reveal what was already behind or around it without introducing an abrupt change. The animation is most useful when its timing supports a clear transition in the story you are telling.
You can also modify the easing curve to change how parameters are interpolated between frames. Easing affects the character of the transition: it changes how the animation progresses between keyframes, while moving the keyframes changes when its stages occur. Adjust one at a time while reviewing the presentation so you can tell whether the pacing or the interpolation is responsible for the result.
A useful troubleshooting checklist: confirm that you selected the intended node; apply the effect to a structural model when changing the transparency of atoms and bonds; and check the keyframe positions if the fade happens at the wrong point in the presentation. These small checks address the most common reasons a fade may not look as expected.
To see the full instructions, visit the SAMSON Disappear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.