Anyone who has worked with complex molecular systems knows that managing atomic structures, ligands, simulations, and annotations can quickly become overwhelming. As molecular modelers, we often lose precious time searching for that one piece of structural data buried deep in a hierarchy, or we end up duplicating work because we can’t easily see what’s already present in a loaded document.
This is where the Document view panel in SAMSON becomes incredibly valuable. It acts as a live organizational map that lets you inspect, filter, and modify the structure of your active molecular document with clarity and control.
What Is Document View?
The Document view displays the hierarchical data graph of the open molecular document in SAMSON. You can think of it like the folder tree in a file browser, but for atoms, residues, molecules, and any objects in your modeling workspace.
Why Use Document View?
Instead of selecting atoms in the 3D viewport one by one, Document view lets you:
- Understand molecular organization at a glance
- Toggle visibility for parts of the model
- Quickly select and isolate nodes (atoms, ligands, etc.)
- Drag and drop nodes to reorganize your data structure
- Apply powerful structural filters using the Node Specification Language (NSL)
Finding What You Need, Fast
The Document view includes a search bar where you can type the name of a node or an NSL expression to quickly filter any part of the hierarchy. This is particularly useful in large protein-ligand complexes where manually navigating through the graphical interface could take minutes.
Multiple Documents, One Place
You can work with several documents at once (e.g., drug candidates, reference proteins, or fragments). Only one is active at a time, and that’s the one shown in the Document view. You can switch between documents using the Home > Documents menu or with a keyboard shortcut.
When Is This Especially Useful?
This tool shines during tasks such as:
- Validating protein structures and identifying residues with issues
- Preparing simulation systems by quickly removing non-essential parts
- Copying and pasting structural groups between files
- Keeping track of annotations, scripts, and embedded files
Tips for Working in Document View
- Use
Ctrl+1(orCmd+1on Mac) to open the Document view quickly - Right-click on any node to access context-specific actions
- Combine with the Inspector and Selection menus for advanced workflows
For modelers working with complex structures or collaborating across disciplines, Document view not only saves time—it helps reduce errors and improves clarity throughout your molecular design workflow.
You can learn more about the Document view and interface tools at 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.