A molecular model can change quickly during interactive modeling. You may drag an atom, relax a structure, or run a simulation—and then realize you need to compare the result with an earlier state. Without a deliberate way to capture those states, it is easy to lose track of what changed or which geometry you wanted to revisit.
In SAMSON, conformations provide a straightforward way to preserve positions for a structural model or a group of atoms. Think of each one as a single frame: it records a state you can return to later. A set of conformations can also be assembled into a path, making it easier to inspect a sequence of structures rather than relying on memory or repeated manual adjustments.
Capture a state before you move on
When you reach a geometry worth keeping, select the structural model or the group of atoms whose positions you want to record. Then choose Edit > Conformation, or press S. SAMSON adds a conformation node to the Document view.
This small step is useful at natural milestones: before and after an edit, after a geometry has relaxed, or whenever you want a reference point for a later comparison. A conformation is a saved position state, not a separate molecular model or a complete simulation history. Naming or organizing your saved states clearly can help you remember why each one matters.
Return to a saved geometry
To restore a saved state, double-click its conformation node in the Document view. You can also right-click the node and choose Restore conformation. This gives you a practical way to revisit a geometry without manually undoing every change that came afterward.
For example, if you are exploring a structure and want to compare a modified arrangement with the starting arrangement, save the starting state first. After making changes, save another conformation. Restoring either state lets you inspect the two geometries in the same working document. The key is to capture the state while it is visible, rather than expecting to reconstruct it later.
Turn snapshots into a path
Individual conformations preserve individual states. To explore them as a sequence, select multiple conformations and right-click the selection. Choose Conformation > Create path from conformations. The conformations must store information for the same set of atoms; this is an important requirement when preparing the states you want to combine.
A useful habit is to decide which atoms you want to track before creating the snapshots, then use that same structural model or atom group for each conformation. If the states were saved for different atom sets, they cannot be combined into a path using this workflow. Once created, the path can be examined further with Path Analyzer.
Keep the work with the document
Conformations are part of the document workflow, so save the document when you want to keep them. When a document is saved as a .sam or .samx file, its conformations are saved as well. That means your useful reference states can remain alongside the model instead of being left as temporary notes or remembered coordinates.
In short: select the atoms you want to track, save a conformation at meaningful points, and combine compatible conformations when you need a path. This turns a series of structural changes into something you can revisit and inspect.
For the full modeling and simulation overview, see the SAMSON documentation on Modeling and Simulation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.