When you open a molecular modeling platform, the first obstacle is not always the molecule. It can be finding the right place to look: the 3D view, the structure tree, an object’s parameters, or the record of what you just changed. If you lose time switching between panels or searching menus, a simple mental map of the SAMSON interface can make your work feel more deliberate.
This guide focuses on a practical goal: quickly orient yourself, find commonly used areas, and shape the workspace around the task in front of you. It is useful whether you are opening SAMSON for the first time or returning after a break.
Start with the workspace map
The interface has several distinct areas, each answering a different kind of question. The viewport shows the document in 3D: it is where you inspect the spatial arrangement of your system. The Document view presents the document’s structure, while the Inspector gives access to parameters for selected nodes, such as atoms, residues, or molecules. The History lists performed actions, helping you review what has happened during a session.
Other areas support different parts of a 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. The menu provides access to commands, workspaces, and open documents, and the status bar may show messages.
Thinking in terms of questions can help you decide where to look: “What does the system look like?” points to the viewport; “What is in this document?” points to Document view; “What are the selected nodes’ parameters?” points to Inspector; and “What actions have I performed?” points to History.
Find a command without browsing every menu
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 available commands, apps, editors, and documentation. This is especially useful when you are still learning the menu or when the installed extensions have added functionality you have not used before.
SAMSON’s interface is constructed from the installed SAMSON Extensions, so the menu reflects the functionality available in your installation. Instead of trying to memorize every menu location, search for the command or tool you need. When you find a command, app, or editor that you use regularly, you can add it to favorites using the star icon shown when hovering over it. Favorites appear in special sections at the top of the ribbon menu and in the Editors viewport menu.
Bring the panels you need within reach
Your workspace does not have to stay in its default arrangement. You can rearrange the Document view, History, and Inspector by dragging their title bars. Widgets can be docked together; to dock or undock one, press its title bar, move it to the desired place, and release the mouse. If a window has a Pin icon, that control can keep the window always on top.
A useful approach is to organize the interface around the immediate task rather than trying to create one perfect layout for every situation. For example, if you are inspecting a structure, keep the viewport and Document view easy to access and bring the Inspector forward when you need to examine selected nodes. If you are reviewing a sequence of edits, make the History panel easy to reach. You can also switch workspaces to change the menu representation. SAMSON saves interface customizations and loads them the next time you open the application.
Use shortcuts to restore panels quickly
When a panel is hidden, a shortcut can be quicker than searching through interface menus. On Windows and Linux, use Ctrl; on macOS, use Cmd. The number identifies the panel:
- Ctrl/Cmd + 1: Document view
- Ctrl/Cmd + 2: Inspector
- Ctrl/Cmd + 3: History
- Ctrl/Cmd + 4: Asset Browser
- Ctrl/Cmd + 7: Animator
Other documented shortcuts include Ctrl/Cmd + 0 for SAMSON AI, + 5 for the Periodic table, + 6 for the Job manager, + 8 for the Python console, and + 9 for the Code Editor. You do not need to memorize the entire list at once. Start with the panels you revisit most often, then add others as they become useful.
A small routine can prevent interface friction from interrupting your modeling: orient yourself by the viewport and Document view, open the Inspector or History when the task calls for it, search for unfamiliar tools with Find everything, and favorite the ones you use repeatedly. The aim is not to keep every panel visible, but to know how to reach the right one quickly.
For a full overview of the interface and its customization options, read the SAMSON “First look: the interface” documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.