When you open a molecular modeling project, the structure itself is only part of the task. You may also need to inspect selected atoms, find a command, review an action, or add a component from an asset library. If you do not yet know where those controls live, even a straightforward modeling task can turn into a search through menus and panels.
SAMSON’s interface is easier to navigate once you connect each area to the job it supports. This quick guide offers a practical way to orient yourself, bring useful panels back into view, and reduce repeated searching.
Start with the workspace map
The main areas have distinct roles:
- Viewport: the three-dimensional view of your document. This is where you see the molecular structure.
- Document view: a structural representation of the document, useful for locating and selecting parts of its hierarchy.
- Inspector: access to parameters for selected nodes, such as atoms, residues, and molecules.
- History: a list of actions performed in the document.
- Asset Browser: access to asset libraries for adding atoms, fragments, and molecules.
- Animator: tools for creating a presentation and adding or modifying animation effects.
- Menu and status bar: the menu provides access to commands and workspaces; the status bar may display messages.
This map helps turn a vague question—“Where did that control go?”—into a more specific one: “Do I need to inspect a selection, review an action, or add an asset?” That distinction makes it easier to choose the right panel.
Bring back a panel with a shortcut
If a panel is hidden, the Interface menu can show or hide interface areas. You can also use the keyboard shortcuts below. On macOS, use Cmd; on Windows and Linux, use Ctrl.
- Ctrl/Cmd + 1: Document view
- Ctrl/Cmd + 2: Inspector
- Ctrl/Cmd + 3: History
- Ctrl/Cmd + 4: Asset Browser
- Ctrl/Cmd + 5: Periodic table
- Ctrl/Cmd + 6: Job manager
- Ctrl/Cmd + 7: Animator
- Ctrl/Cmd + 8: Python console
- Ctrl/Cmd + 9: Code Editor
- Ctrl/Cmd + 0: SAMSON AI
A simple workflow is to open only what you need for the current task: Document view and Inspector when working with a selection, History when you want to review actions, or Asset Browser when building a system. When you are done, you can hide or rearrange panels to make room for the viewport.
Make the layout fit your work
The Document view, History, Inspector, and many extension widgets can be docked together. To move a widget, press its title bar, drag it to the desired location, and release the mouse. Some windows, including certain Apps, may offer a pin icon to keep them on top.
You can also switch workspaces to change how the menu is represented. The layout you customize is saved and loaded the next time you open SAMSON, so arranging panels around a recurring task can save you from setting them up again each session.
Search first; favorite what you use often
The Find everything box at the top of the menu searches available commands, apps, editors, and documentation. It is a useful starting point when you know what you want to do but not which menu contains the tool. Search results can also be added to favorites by clicking the star that appears when you hover over them.
Favorites appear in special sections at the top of the ribbon menu and in the Editors viewport menu. This gives frequently used items a more direct route without requiring you to remember where they are in the menu. Click the star again to remove an item from favorites.
One useful habit is to search for a tool when you first need it, then favorite it if you find yourself returning to it. Over time, this creates a workspace that reflects your own modeling routine instead of one you have to navigate from scratch.
For a panel-by-panel reference and further orientation, read First look: the interface.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.