When you open a molecular modeling project, the structure itself is only part of what you need to work with. You may also need to inspect selected atoms, review an earlier action, find a tool, or add a molecule from a library. If you are still learning the interface, it is easy to spend time searching for the right panel instead of working on the model.
A useful first step is to connect each task with the part of the SAMSON workspace designed for it. Once you know that map, the interface becomes easier to navigate—and easier to recover when a panel is hidden or your layout feels unfamiliar.
Start with the three areas you use to orient yourself
The viewport is the three-dimensional view of your document. It is where you see the molecular structure. The Document view shows a representation of the document’s structure, while the Inspector provides access to parameters for selected nodes, such as atoms, residues, and molecules.
These views answer different questions. If you are asking, “What does the model look like?”, start in the viewport. If you need to understand or select something within the document structure, look to the Document view. If you have selected a node and need to inspect its parameters, use the Inspector.
Use History when you need to retrace your steps
The History lists actions that have been performed. It can help when you want to review what has happened during a session rather than trying to remember each operation. The status bar may also display messages, so it is worth noticing when the application provides feedback there.
Other panels support specific parts of a modeling workflow. The Asset Browser provides access to asset libraries for adding atoms, fragments, and molecules. The Animator is for creating presentations and adding or modifying animation effects. Knowing these roles helps you choose a starting point without opening panels at random.
Find tools instead of hunting through menus
When you know what you want to do but not where its command lives, use Find everything at the top of the menu. It can search for available commands, apps, editors, and documentation. The shortcut shown in the documentation is Shift + E.
You can also mark commands, apps, and editors as favorites from the search results by clicking the star that appears when you hover over them. Favorites appear in dedicated sections at the top of the ribbon menu and in the Editors viewport menu. This is a practical way to make frequently used tools easier to reach without needing to remember which menu contains each one.
Bring back a panel with a shortcut
If a panel is missing, use the Interface menu or its shortcut rather than assuming it has disappeared from the application. The documented shortcuts are Ctrl + 1 for Document view, Ctrl + 2 for Inspector, Ctrl + 3 for History, Ctrl + 4 for Asset Browser, and Ctrl + 7 for Animator. On the Mac shortcut column, use Cmd with the same number. The shortcut table also lists SAMSON AI, Periodic table, Job manager, Python console, and Code Editor.
Panels can be rearranged by dragging their title bars. Widgets can be docked together, or moved to another position; release the mouse where you want the panel to sit. Some windows, including certain Apps, may also have a Pin icon to keep them on top. If you customize the layout, SAMSON saves it and loads it the next time you open the application.
A simple recovery routine is therefore: search for the tool, use the relevant shortcut if a panel is hidden, and reposition a panel by dragging its title bar if the layout is inconvenient. The interface can also change according to the selected workspace, which modifies how the menu is represented.
A small orientation checklist
- Need to see the structure in 3D? Go to the viewport.
- Need to examine the document’s structure? Use Document view.
- Need parameters for a selected node? Open the Inspector.
- Need to review performed actions? Check History.
- Need a command or editor? Search with Find everything.
- Need to add molecular building blocks? Open the Asset Browser.
This quick map should make it easier to get back to the science when the interface feels unfamiliar. For the complete panel reference and additional details, learn more in the SAMSON first-look guide.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.