When working on multi-layered molecular design projects, clarity and structure are essential. Whether you’re modeling a protein-ligand interaction or managing multiple systems in parallel, organizing your data hierarchy efficiently can save hours of repetitive work—and more importantly, reduce error. That’s where the Document view in SAMSON becomes indispensable.
The Document view offers a tree-based representation of your active document—what SAMSON refers to as the hierarchical data graph. For molecular modelers, this means a clear, expandable structure that mirrors the molecular and experimental complexity you’re working on.
Why is Document View important?
Let’s say you’re working on a protein complex with multiple ligands and water molecules, and you also want to test variations across different conformational states. Without a system to manage this efficiently, it’s easy to lose track of nodes, accidentally edit the wrong structure, or export the wrong data.
The Document view solves this by letting you:
- Visualize your project as a tree, making it easier to understand relationships among atoms, residues, chains, and higher-level structures.
- Quickly select, show/hide, or modify nodes directly from the hierarchy.
- Use filters and the Node Specification Language (NSL) to target specific parts of your system.
- Drag-and-drop nodes to restructure your document intuitively.
Useful Actions at Your Fingertips
Each node within the document view comes with a context menu and a context toolbar accessible by right-clicking. Whether you want to add a visual model to a selected chain or reassign a group of atoms to a new folder, you can do that without navigating through multiple menus.
This hierarchical view also lets you rename nodes for clarity, or apply structure-level commands (like visualization presets or property editing) directly.
Effortlessly Switch Between Documents
Another pain point in molecular modeling software is managing multiple files. In SAMSON, not only can you have multiple documents opened at once, but the Document view clarifies which one is currently active based on the view.
You can switch open projects by:
- Clicking the Documents list in the top-left corner of the menu,
- Using
Home > Documents, or - Shortcut:
Ctrl+TaborCmd+Tabfor Mac users.
This is especially useful if you’re referencing one structure to build another, or comparing variants under different conditions.
Helpful Visual Feedback
See your edits in real-time. Select atoms or residues from the Document view and they’ll be highlighted in the 3D viewport. It works the other way too—make a selection in the viewport, and the corresponding elements light up in the Document view.
Example: Selecting Nodes with Precision
Need to modify several binding site residues at once? Use the Document view’s filter bar to quickly find them by name or NSL criteria. Then, apply actions like highlight, colorize, or group.
How to Open Document View
Access the Document view by navigating to Interface > Document view or by using the shortcut:
Ctrl+1(Windows/Linux)Cmd+1(Mac)
Once open, the left sidebar will display the full data hierarchy of your molecular system, allowing smooth navigation and efficient management.
Final Thoughts
For anyone modeling polymers, macromolecular assemblies, or preparing complex simulation inputs, the Document view helps you stay in control. It’s not just about navigating your project—it’s about doing it with confidence and precision.
To learn more, visit the full documentation page at https://documentation.samson-connect.net/users/latest/interface/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.