When working with molecular models, visualizing movements is often crucial to understanding molecular function. Whether you’re studying conformational changes, ligand docking pathways, or simply presenting your simulation results, clear and intuitive animations can help tell a more compelling story — both to yourself and your audience.
One recurring challenge many molecular modelers face is the need to rotate a group of particles smoothly around its center to better grasp spatial relationships or highlight molecular mechanisms. Instead of constructing such movements manually frame-by-frame, which can be both time-consuming and imprecise, SAMSON offers a built-in solution: the Rotate animation effect.
The Idea Behind the Rotate Animation
The Rotate animation lets you rotate any group of particles around its geometric center, automatically calculating the centroid and applying a clean rotation around an axis aligned with the Z-axis. This is ideal for illustrating processes like protein domain swiveling or nucleic acid twisting, or even just giving your audience a better view of a molecular surface or pocket.
Step-by-Step: Adding the Rotate Animation
Here’s how to get started with a Rotate animation in SAMSON:
- Select the group of particles you would like to rotate. This might be a side chain, a ligand, or a whole domain – whatever makes sense for your model.
- Open the Animation panel in the Animator.
- Double-click on the Rotate animation effect. This will insert a Rotate effect between two keyframes.
- Adjust the keyframes to define the duration and extent of rotation. The more frames between the keyframes, the smoother the animation will feel.
You can always move the keyframes later on, so don’t worry if the timing doesn’t feel perfect on first try.
Customization with Easing Curves
If you want a more natural feel to your animation — for example, starting slow and gaining speed — you can customize the interpolation behavior using Easing curves. This adds to the realism and makes your animations feel less mechanical.
One thing to keep in mind: if you’ve previously used SAMSON, you might remember animations being accessed via a dedicated Animation menu. That menu has been replaced. All effects, including Rotate, are now accessible via the Animation panel in the Animator, streamlining the workflow.
When Is This Useful?
Here are a few scenarios where the Rotate animation proves useful:
- Highlighting a pocket or binding site: Rotate part of a molecule to give viewers a clear view inside.
- Explaining molecular mechanisms: Show rotational movement that mimics conformational changes in a protein complex.
- Building educational content: Guide students’ attention to molecular features through slow and controlled spins.
Whether you’re prepping for a conference talk or making a tutorial for your research group, this simple-to-use animation can make a significant difference.
To learn more about how to set it up, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/rotate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.