For molecular modelers dealing with multi-component systems, navigating and organizing complex structures can be time-consuming and error-prone. Whether you’re working with large protein complexes, nucleic acids, or synthetic compounds, keeping control over your molecular hierarchy is key to productivity — and clarity.
SAMSON offers a solution to this problem through its Document view, a powerful hierarchical browser designed to help users inspect, navigate, and manipulate molecular data with precision. However, many users overlook this feature or use only its basic functionality.
Why the Document View Matters
When you’re building or editing molecular systems in SAMSON, structures often contain multiple levels of hierarchy: atoms belong to residues, which belong to chains, which might be part of a larger assembly. Documents can quickly become difficult to manage, especially when multiple structures are loaded in parallel. The Document view gives you full visibility over this data graph and lets you interact with it in a structured way.
Key Features of the Document View
- Visual Hierarchy: Instantly see how atoms, residues, chains, molecules and annotations are organized within your project.
- Node Filtering: Use the Filter nodes… box to dynamically search through node names or types, accelerating selection workflows.
- Context Actions: Right-click any node to access specific actions such as hiding, renaming, duplicating, exporting, or preparing the selection.
- Drag & Drop: Rearrange nodes and groups by simply dragging them to move parts of your structure into new organizational groups.
- Multi-Document Management: Quickly switch between open documents via the top menu or the Home > Documents menu. Each document has its own Document view.
Even better, many actions update the selection and visualization instantly — a handy feedback loop when working with complex systems.
Common Use Cases
1. Selecting Specific Chains in Large Protein Structures
Instead of navigating visually in the viewport, select specific chains or domains from the Document view. This is especially useful in multi-chain protein-ligand complexes or when comparing conformations.
2. Hiding Non-Essential Parts
Quickly hide ligands, water molecules, or ions by selecting them in the Document view and choosing “Hide” from the context menu. This helps isolate your structure of interest for visualization or simulation.
3. Creating Custom Groups
Customize your data graph by organizing nodes into meaningful folders. This improves project readability when revisiting files after weeks or sharing them with collaborators.
4. Advanced Selection
Couple the Document view with SAMSON’s selection tools to refine your selection by residue ID, chain, or molecular groupings. This is particularly effective when coupled with visual presets and simulation tools.
Shortcuts to Remember
- Windows/Linux:
Ctrl + 1to toggle the Document view - Mac:
Cmd + 1
With these features, the Document view in SAMSON becomes more than a tree structure — it acts as your command hub for structure-driven modeling. Whether you’re performing selections, adjusting visibility, or preparing a file for export and sharing, it’s the place where you regain understanding of your molecular system.
To explore more document management features, visit the official documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. To download SAMSON, visit www.samson-connect.net.