Molecular modelers often need to compare different structural states of a molecule—whether it’s to analyze intermediate steps of a simulation, visualize reaction pathways, or share reproducible milestones in a modeling workflow. However, managing these snapshots within a single project has traditionally required exporting multiple files or relying on custom scripts.
Conformations in SAMSON provide a native, integrated solution to this problem. With conformations, you can easily store, access, and transition between different states of your molecular system directly within the SAMSON document. It’s a simple yet powerful way to capture the progress of your simulations or modeling sessions.
What is a Conformation?
In SAMSON, a conformation is essentially a saved state—a snapshot of the positions of atoms in a structural model at a given moment. Think of it like a single frame in a molecular movie. Each conformation can be restored later or even combined into a continuous path.
When Would You Use Conformations?
- Tracking changes during interactive simulations
- Capturing before-and-after states of geometry optimizations
- Comparing alternative conformers of a molecule
- Saving intermediate results in a multi-step modeling process
- Preparing image sequences or animations
How to Save a Conformation
Saving a conformation is straightforward:
- Select the structural model or group of atoms you wish to capture.
- Click Edit > Conformation, or simply press the S key.
A conformation node will then appear in the Document view, storing the selected positions:
Restoring and Managing Conformations
To restore a saved conformation, double-click on it in the Document view. Alternatively, right-click on the conformation and choose Restore conformation from the menu:
You can keep multiple conformations to easily switch between them during your modeling session.
Creating Paths from Conformations
If you have several conformations for the same set of atoms, you can generate a trajectory or animation path:
- Select all conformations you wish to use.
- Right-click the selection and choose Conformation > Create path from conformations.
This is particularly useful for visualizing how a molecular system evolves, for example during energy minimization or in response to user interaction.
Additional Notes
- Conformations are saved along with your document in .sam or .samx files—no extra export required.
- You can visually organize conformations in the Document view using folders or labels.
Whether you’re preparing a paper, analyzing reaction dynamics, or just experimenting with molecule editing, SAMSON’s conformation system helps you keep track of every important configuration.
Learn more about modeling and simulation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.