A molecular structure can be difficult to follow when it appears all at once—especially in a presentation where you want viewers to focus on one part of the scene before taking in the rest. In SAMSON, the Appear animation offers a gradual alternative: selected nodes transition from transparent to opaque over time.
This can help make a reveal easier to follow, but it also helps to know exactly what the animation affects. The key is to apply it to the right kind of node and to arrange its keyframes around the moment you want the structure to become visible.
Choose the right node first
Appear works on nodes that have a transparency attribute. Examples include structural models, visual models, meshes, and labels. If a node has no transparency attribute, the animation behaves similarly to the Show animation instead.
One detail is particularly important when working with atoms and bonds: individual atoms and bonds do not have their own opacity attribute. Their structural models do. So, if your goal is to fade in atoms and bonds, apply Appear to the relevant structural model, rather than selecting individual atoms or bonds and expecting their transparency to change.
Build the reveal
- Select the nodes you want to reveal.
- Open the Animation panel in the Animator.
- Double-click the Appear animation effect to add it to the selected nodes.
- Review the animation’s four keyframes and move them as needed to fit your presentation.
The four-keyframe sequence defines the basic visual progression. Between keyframes 1 and 2, the chosen nodes are fully transparent. Between keyframes 2 and 3, they progressively appear as their transparency decreases. Between keyframes 3 and 4, they remain fully opaque. In other words, the reveal happens in the middle portion of the sequence, with a transparent lead-in and an opaque ending.
Make the timing work for your explanation
The animation’s keyframes can be moved, so you are not limited to leaving the reveal at its default timing. For example, you can arrange the sequence so the transparent phase comes before the moment you begin discussing a model, then give the gradual appearance enough time to be noticed. The right pacing depends on what your audience needs to see; the useful principle is to make the reveal support the explanation rather than compete with it.
You can also change how parameter values are interpolated between frames by modifying the Easing curve. This affects the progression between keyframes, while moving the keyframes changes where those stages occur in the animation. If the reveal feels too abrupt or too drawn out, these are the documented controls to review.
A quick troubleshooting check
If the selected atoms or bonds do not fade as expected, check whether you applied the animation to their structural model. If a node does not support transparency, expect behavior similar to Show rather than a gradual transparency change. These two checks can prevent a common mismatch between what you selected and what the animation can visually change.
For the full instructions, see the Appear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.