When you adjust a molecular structure, the latest coordinates can quickly replace the arrangement you wanted to compare against. That makes a simple question surprisingly difficult: What did the model look like before that change? In SAMSON, conformations offer a straightforward way to save and revisit molecular states while you work. A conformation stores the positions of a structural model or group of atoms—like one frame in a trajectory.
This is useful during interactive modeling, geometry changes, or any workflow where you want to preserve a meaningful arrangement before continuing. Rather than relying on memory or trying to recreate a pose, you can save it in the document and restore it when needed.
Make a checkpoint before you change the structure
First, select the structural model or group of atoms whose current positions you want to preserve. Then choose Edit > Conformation, or press S. SAMSON adds a conformation node to the Document view.
A practical habit is to save a conformation at a moment that has a clear meaning: before an adjustment, after a geometry optimization, or when you reach a pose you may want to revisit. Give the saved state a role in your workflow by treating it as a checkpoint, not merely as another item in the document.
Return to a saved state
To restore a saved conformation, double-click it in the Document view. Alternatively, right-click the conformation and choose Restore conformation.
This gives you a reliable way to return to the saved positions while exploring alternatives. For example, you can preserve a starting arrangement, make a change, and then restore the earlier state if you want to compare or try a different direction. The conformation records positions; it is not, by itself, a complete record of every action that led to them.
Turn saved states into a path
If you have several conformations and want to examine them as a sequence, you can create a path from them. The key requirement is that the conformations must contain position information for the same set of atoms. This is worth checking before combining states: a path is intended to connect matching atoms across the saved conformations.
- Select the conformations you want to combine.
- Right-click the selection.
- Choose Conformation > Create path from conformations.
Once created, the path can be explored with Path Analyzer. In practice, this creates a useful distinction: save individual conformations when you need specific checkpoints, and combine compatible conformations into a path when you want to explore a sequence of states.
Keep your checkpoints with the document
Conformations are document nodes, so they fit into the same working document as the structure. When you save a document as a .sam or .samx file, its conformations are saved as well. That makes them available when you reopen the document, rather than leaving important states only in your memory or in an unsaved session.
A compact workflow to remember: select the atoms or model, press S to save a conformation, continue modeling, and restore the saved state when you need to return. When you have multiple conformations for the same atoms, combine them into a path for further exploration.
For the full modeling and simulation overview, see the SAMSON Modeling and Simulation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.