A molecular modeling session can get messy in a familiar way: several documents are open, the structure has many nested parts, and the panel you need has disappeared behind another window. The challenge is not only finding a command. It is keeping track of which document you are working in, what you have selected, and where to inspect or change it.
SAMSON’s interface includes a few useful anchors for that situation: the Document view for navigating a structure’s hierarchy, the Inspector for examining selected nodes, and the History view for returning to an earlier undoable state. Here is a simple workflow that uses them together.
1. Confirm the active document
You can have several documents open, but only one is active at a time. The active document is the one shown in the Document view. Before editing, take a moment to confirm that it is the document containing the molecule you intend to work on. Switch documents from the Documents list near the top-left of the menu, or use Ctrl/Cmd + Tab to cycle forward and Ctrl/Cmd + Shift + Tab to cycle backward.
This small check can prevent a surprisingly costly mistake: making a valid edit to the wrong open structure. The Home menu also provides access to the open Documents list.
2. Use the Document view to orient yourself
The Document view displays the active document as a hierarchical data graph. Open it from Interface > Document view, or use Ctrl + 1 on Windows and Linux, or Cmd + 1 on Mac.
Rather than trying to pick a tiny object directly in a crowded molecular view, use the hierarchy to locate and select nodes. The Document view can also show or hide nodes, filter by node names or with Node Specification Language, and let you reorganize the document by dragging and dropping nodes. Context menus and context toolbars offer actions for specific nodes.
When the hierarchy is unfamiliar, filtering is a useful first step: narrow the list to relevant names or node types, then select the item you want to examine. This gives you a clearer route from the overall document structure to a particular component.
3. Inspect the selection before changing it
Once you have selected nodes, open the Inspector from Interface > Inspector. Its shortcuts are Ctrl + 2 on Windows and Linux and Cmd + 2 on Mac. The Inspector displays properties of selected nodes and can edit them. Keep in mind that it applies to all selected nodes, not just one. If you intended to change a single atom or other node, check the selection before editing.
You can use the Inspector’s filter to show matching attributes only, which can make a long list of properties easier to work with.
4. Treat History as a checkpoint, not a guarantee
The History view lists undoable operations. Open it from Interface > History, with Ctrl + 3 on Windows and Linux or Cmd + 3 on Mac. Selecting an entry returns the document to its associated state, making History helpful when you need to review recent changes or step back from an operation.
There is an important limitation: not every operation is undoable. If a non-undoable operation occurred between undoable ones, SAMSON may not be able to restore the document as expected. For that reason, do not assume History is a complete substitute for saving your work. Use it to navigate the undoable steps you can see, and save important document states as part of your workflow.
A quick recovery routine
- Check which document is active.
- Open the Document view and locate the relevant nodes.
- Confirm the selection before editing; inspect it in the Inspector if needed.
- If an edit needs to be reversed, review the History view and remember that not all operations are undoable.
This routine helps address three common sources of confusion—wrong document, wrong selection, and uncertainty about recent edits—without requiring you to memorize every menu. For more details on the interface and its panels, see the SAMSON Interface documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.