When working on complex molecular modeling projects, keeping track of multiple structures, simulations, and variations can become challenging. If you’ve ever found yourself digging through layers of molecules trying to remember where you left that optimized ligand structure, you’re not alone. Luckily, SAMSON offers a feature designed specifically to help you manage this complexity: the Document view.
This tool is something like a project dashboard—it shows a hierarchical data graph of your active document and allows you to interact with its components in a very intuitive way. It’s especially helpful when working with large biomolecular systems or managing multiple conformations, molecular designs, or simulations within one session.
Why the Document View Matters
When dealing with molecular systems, users often face these common issues:
- Difficulty switching between different molecular models or simulation setups.
- Time-consuming navigation through layered molecular data.
- Inability to quickly isolate specific residues, atoms, or ligands for visualization or editing.
The Document view solves these problems by visually mapping every element in your active SAMSON document in a tree structure. This makes it easier to:
- Quickly locate and select nodes (e.g., molecules, chains, groups).
- Show or hide specific parts of the system with one click.
- Reorganize structures using drag-and-drop.
- Filter elements using names or the Node Specification Language (NSL).
How It Works
To open the Document view, go to Interface > Document View or use the shortcut Ctrl+1 (or Cmd+1 on Mac). You’ll see a window displaying the structure of your active document — proteins, ligands, water molecules, etc. are nested in an expandable tree format.
You can:
- Click to isolate or highlight specific parts in the viewport.
- Right-click for context-specific actions such as renaming, converting, or deleting.
- Drag nodes to nest them elsewhere—for example, moving a ligand into a different folder.
This is especially helpful if you’re building up custom molecular assemblies or evaluating multiple versions of the same system. You might want to compare apo and holo forms of a protein, or different docking poses — simply store them in different hierarchies within one document and switch between them as needed.
Combining Multiple Documents
If you want to keep various workflows separate but still accessible, SAMSON lets you open several documents at once. Only one is active at any given time (i.e., the one shown in the Document view), but switching between them is fast:
- Use the Documents list in the top-left corner of the interface.
- Navigate via the Home > Documents menu.
- Or use keyboard shortcuts:
Ctrl+TaborCtrl+Shift+Tab(orCmdequivalents).
This setup allows you to run simulations in one document while preparing visualizations in another — all without clutter or confusion.
Helpful Filters and Tools
The Document view includes a filtering function that lets you search for specific node names or use NSL to create custom queries (e.g., select all ligands or charged residues). Combined with the viewport, it becomes a powerful interface to manipulate large datasets more effectively.
Whether you’re validating a protein structure, running an interactive simulation, or preparing a figure for publication, the Document view can help you stay organized and focused.
To explore all the features of the Document view and other useful interface tools, visit the SAMSON Interface documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.