When exploring molecular systems, many researchers face the challenge of navigating between different conformations—a particular geometric state of a molecule. Whether tweaking a ligand’s side chain or optimizing a nanotube’s structure, saving stable intermediate positions can be surprisingly valuable. If you’ve ever needed to keep track of how your molecule evolved or wanted to revert to a prior shape, SAMSON’s conformation system can make your workflow significantly smoother.
In SAMSON, a conformation is essentially a snapshot of the positions of atoms in either a structural model or a group of atoms. Think of it as bookmarking a 3D shape—allowing you to revisit it later, compare different states, or even animate transitions between them.
Why conformations matter
Conformations help you:
- Revert a molecule to a previous shape
- Compare multiple candidate structures
- Build animations from discrete transformation steps
- Store progress through interactive simulations
How to save a conformation
The process is simple:
- Select the structural model or group of atoms whose conformation you want to save. Use the selection tools as described in the Selecting section of the documentation.
- Click Edit > Conformation or simply press S on your keyboard.
Once done, you will see a new conformation node appear in the Document view:
Restoring conformations
You can restore a conformation whenever needed by either:
- Double-clicking on the conformation node in the Document view
- Right-clicking the node and selecting Restore conformation
This allows for quick toggling between different structural states. For example, if you are comparing minimized versus non-minimized structures or observing how a molecule deforms under force interactions, restorability becomes particularly handy.
Building a trajectory from conformations
If you have multiple conformations saved for the same set of atoms, SAMSON lets you combine them into a path—a sequence of frames that essentially become an animation of your molecule.
- Select the conformations of interest in the Document view.
- Right-click and select Conformation > Create path from conformations.
This feature is particularly useful for visualizing the change between different states, making it easier to prepare illustrative figures or videos, or even for inspecting local minima in conformational analysis.
A note for saving your work
When you save your SAMSON document files as .sam or .samx, all your saved conformations are preserved too. This allows you to resume your project later with full access to all previously saved states.
To learn more about conformations and how to work with them in SAMSON, view the full documentation here: https://documentation.samson-connect.net/users/latest/modeling-and-simulation/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.