A molecule moves during interactive modeling, but a visual change alone can be hard to interpret later. Which geometry did you start with? What did the structure look like after relaxation? If you want to revisit a state—or turn several states into a trajectory—you need to preserve the positions as you work.
In SAMSON, conformations provide a simple way to keep these snapshots in the document. A conformation stores the positions of a structural model or group of atoms, much like one frame in a trajectory. It is useful when you want to record a starting geometry, capture a meaningful intermediate, or retain a result before making further changes.
First, make the structure move
To try this workflow, start with a small system. Add a molecule from the Asset Browser, or use the Add editor to place an atom in the viewport. Then choose Edit > Add simulator. For the example in the SAMSON documentation, select Universal Force Field as the interaction model and Interactive modeling as the state updater.
Start the simulation with Edit > Start simulation or press X. While it runs, you can still act on the atoms: select an atom and drag it slowly to see the molecule respond. This is useful for hands-on modeling, but it also means the structure can change as you work. Treating important moments as explicit snapshots helps make those changes easier to revisit.
When you want to pause, choose Edit > Stop simulation or press X again. The same shortcut starts and stops the simulation, so check its current state before continuing.
Save a state before it disappears
To capture the current geometry, select the structural model or the group of atoms you want to record, then choose Edit > Conformation or press S. A conformation node appears in the Document view. Give yourself useful checkpoints: for example, save the initial geometry before manipulation, then save again after a change you want to compare or keep.
A saved conformation is not a separate molecular model; it is a stored position state for the selected atoms. To return to it, double-click its node in the Document view, or right-click and choose Restore conformation. This makes it easier to compare alternatives without relying on memory or trying to reproduce a hand-dragged arrangement.
Turn snapshots into a path
Several conformations can also become a path—a trajectory you can explore as a sequence. The key requirement is that the conformations store information for the same set of atoms. Select the conformations, right-click, and choose Conformation > Create path from conformations. Once created, the path can be explored with Path Analyzer.
This sequence—save a state, make a change, save another state, then combine compatible snapshots—helps turn an interactive modeling session into something you can inspect again. It is especially helpful when geometry changes are gradual: a few named checkpoints can make the progression easier to understand than one final structure alone.
Conformations are stored with the document when you save it as a .sam or .samx file. For the full explanation of simulators, conformations, and paths, see the SAMSON Modeling and Simulation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.