Progressive Disappearance in Molecular Models: A Clearer Way to Present Complex Structures

When preparing molecular animations for presentations or publications, clarity and focus are essential. One of the common challenges molecular modelers face is how to gently de-emphasize or hide specific parts of a model without abruptly removing them. A sudden disappearance can distract or confuse the viewer. That’s where the Disappear animation in SAMSON comes in.

The Disappear animation solves this by gradually increasing the transparency of selected model components over time, enabling smoother transitions and cleaner visuals during animations. Whether you’re working with structural models, visual models, meshes, or even labels, this feature helps direct attention exactly where you want it, when you want it.

Why Use Disappear Instead of Hide?

At first glance, the Hide animation might seem to fulfill the same purpose. However, the key difference is transparency. The Disappear animation allows selected nodes to gradually become transparent over a specified duration, rather than simply vanishing between frames. This can be much more helpful when you want viewers to see what’s hidden underneath a disappearing model, such as binding sites, reaction mechanisms, or alternate conformations.

More specifically, the Disappear animation works on nodes that have a transparency attribute. These include:

However, remember that individual atoms and bonds do not have a transparency attribute. If you want to make them disappear, apply the animation to their corresponding structural models instead.

How It Works

To create a Disappear animation:

Select the nodes you want to fade out.
In the Animation panel of the Animator, double-click on the Disappear effect.

The animation includes 4 keyframes:

From keyframe 1 to 2: nodes remain fully visible (opaque)
From 2 to 3: nodes gradually fade, increasing transparency
From 3 to 4: nodes become fully transparent

You can adjust the position of these keyframes to control the timing of the effect. Also, it’s possible to fine-tune the way the transparency changes over time by modifying the easing curve.

Example in Action

Here’s a visual example of the Disappear animation at work:

This example shows the gradual disappearance of part of a model, making it easier to reveal inner structures while retaining a smooth visual experience.

When to Use It

Consider using the Disappear animation when:

You want to progressively introduce or remove layers of your model
You’re highlighting a change over time without abrupt transitions
You want to guide attention through storytelling in molecular animations

To learn more, visit the official documentation page here: Disappear Animation Documentation

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.