Working with complex molecular systems isn’t just about atom placements or energy calculations—it’s also about staying organized. When you’re managing multiple structures, simulations, and design components, locating and modifying specific parts of your system efficiently becomes a challenge. That’s where the Document view in SAMSON can make a difference.
In SAMSON, every molecular design resides in a document—a structured container where molecules, simulations, annotations, and more coexist. But what happens when the system becomes large and you need to make sense of what’s inside?
The Document View: An Interactive Map
The Document view gives users a hierarchical graph of the active SAMSON document, showing nodes for atoms, molecules, folders, annotations, and more—all visually structured so you can see how everything fits together.
Think of it as a molecular outline view—you get to expand and collapse levels, show or hide nodes, and drag-and-drop components to restructure your work.
Benefits for Molecular Modelers
- Quick selection: Click any node to select it in the viewport. Great for navigating large systems without manual selection.
- Search and filter: Use names or even SAMSON’s advanced Node Specification Language to filter down to what you need.
- Clean organization: Organize your document logically with folders, notes, and groups to keep simulations, ligands, or model variants separated.
- Apply actions: Right-click on any node for context-specific actions, such as hiding structures, assigning properties, or visualizing them differently.
Working with Multiple Documents
You can have several documents open at once—helpful when comparing structures, copying components, or managing templates. To switch between opened documents, use Ctrl/Command + Tab (or Shift + Tab for reverse). You’ll see a dropdown list in the Home > Documents section or at the top-left of the window.
More Than Just a Tree
The Document view also integrates with SAMSON’s visualization and editing tools. For instance:
- Automatically highlight selections across the interface: select something in the document view and it’s reflected in the viewport.
- Change visibility without altering your entire scene.
- Easily inspect or edit attributes of selected nodes.
Why It Matters
Whether you’re assembling a protein-ligand complex, reviewing output from a simulation, or building a database of molecules, clutter and confusion slow you down. The Document view helps keep your workspace navigable, saving time and reducing possible mistakes.
Learn more about SAMSON’s interface here: https://documentation.samson-connect.net/users/latest/interface/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.