Animations play a crucial role in communicating complex concepts in molecular modeling. However, a common challenge arises when trying to illustrate scenarios where some atoms need to stay put while others move—such as docking, conformational changes, or assembling molecular complexes. In such cases, uncontrolled movement can make it difficult to draw attention to the right parts of your system or convey the intended message. This is where the Hold atoms animation in SAMSON can make a big difference.
The Hold atoms effect lets you freeze the positions of selected atoms between two keyframes within an animation. This allows you to create clearer and more focused presentations—ideal not only for better visualization but also for educational purposes, publications, and team collaboration.
When would a molecular modeler need this?
Imagine preparing an animation that shows the docking of a ligand to a receptor. If the entire receptor also shifts while the ligand moves, it can be visually confusing. Using the Hold atoms animation, you can freeze the receptor’s atoms in place while highlighting only the ligand’s motion. This keeps your audience’s focus where it matters the most.
How to Use “Hold atoms” in SAMSON
- First, select the group of atoms you want to remain fixed.
- Then, in the Animator, double-click on the Hold atoms animation effect in the Animation panel.
- Place two keyframes on the timeline—before and after the time period you want the atoms to stay fixed. The atoms will hold their position between these keyframes.
- You can reposition the keyframes at any time to adjust the duration of the hold effect.
Practical Example
The image below illustrates the combined use of the Move atoms and Hold atoms effects. Here, a molecule bends while part of its structure remains locked in space, making for a visually clear motion sequence.
Where to See Examples
You can find working presentations using the Hold atoms effect on SAMSON Connect Documents. A few examples include:
Whether you’re illustrating mechanisms or building educational content, the Hold atoms tool provides a fast and intuitive way to gain control over your molecular animations.
To learn more, visit the official documentation page here: Hold atoms – Animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.