Creating effective visual presentations of molecular systems can be time-consuming. One common challenge molecular modelers face is clearly showing how individual components of a complex structure come together. Whether preparing figures for a paper or animations for a presentation, clearly conveying the organization of atoms, molecules, or molecular complexes can be tricky.
This is where the Assemble animation in SAMSON can help. This animation makes selected nodes or meshes systematically move into their final configuration from automatically calculated positions away from the original. The result is a visually intuitive transition that helps highlight structural organization without requiring manual setup of start or end states.
Why This Helps
When presenting molecular structures to colleagues or students, or even when analyzing them yourself, static images often don’t tell the full story. Showing atoms or molecules dynamically coming together provides a better sense of spatial arrangement and function. Rather than manually animating separate parts, the Assemble animation saves time by automatically computing motion vectors and interpolating positions.
How to Use Assemble
Using the Assemble animation is simple and requires just a few steps:
- Select a group of structural nodes or meshes in your SAMSON document. If no selection is made, SAMSON attempts to infer the relevant objects.
- Go to the Animator, locate the Animation panel, and double-click on the Assemble effect.
- Two keyframes will be automatically created. The selected nodes will move from displaced starting positions to their current positions between those frames.
- Adjust the keyframes to control when the animation starts and ends. For finer control, open the Inspector to change parameters like amplitude or the easing curve for interpolation.
Tips and Flexibility
You can customize the Assemble animation in several ways:
- Change how dramatically components move by editing the amplitude in the Inspector.
- Fine-tune how the animation feels using different easing curves, such as linear, ease-in, or ease-out, depending on whether you want a smooth start or finish.
- The animation is not limited to atoms—you can apply it to any structural node or mesh, making it versatile for diverse molecular scenes.
See It in Action
An example of the Assemble animation shows how atoms intuitively converge from a scattered formation back into a meaningful structure:
You can also explore existing SAMSON documents using this animation, such as:
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.