Molecular modeling projects often involve not just atoms and molecules, but hierarchical systems comprising proteins, ligands, solvents, ions, and other components. When working with such complex structures, users frequently struggle with clarity and navigation—especially when tracking changes or analyzing subcomponents.
This is where SAMSON’s Document View becomes essential. It offers a clear, interactive representation of molecular structures as a hierarchical data graph, so you can see how every part of your system fits together—enhancing both accuracy and efficiency in your modeling workflows.
Why Document View Matters
The Document View is SAMSON’s central panel for understanding and organizing your active molecular system. This view gives you a structured breakdown of every node present in your document: atoms, residues, molecules, visual elements, annotations, simulations, and scripts—all accessible in a tree-based format.
Whether you’re visualizing a simple molecule or assembling a complex protein-ligand-solvent system, the Document View helps you:
- Quickly view and explore the document’s hierarchy
- Find specific elements using filters
- Show or hide specific components
- Select parts of the system for editing or inspection
- Drag-and-drop nodes to reorganize your molecular system
Example: Refining a Protein System
Let’s say you’re working with a protein-ligand complex. You fetched the structure from the Protein Data Bank and want to remove water molecules, inspect ligands, and highlight specific residues.
In the Document View, you can:
- Unfold the structure tree to locate chains, ligands, or solvents
- Right-click to hide unwanted elements like water molecules
- Use the Filter nodes field to find components with specific names or properties
- Click to select parts of the system and use the Inspector panel to modify properties or apply visual effects
Switching Between Documents
SAMSON supports working with multiple documents, each potentially containing different systems or versions. The Document View lets you instantly switch between them using the Home > Documents menu or by using keyboard shortcuts like Ctrl+Tab. You can also see how many documents are currently open and stay in control of your workspace.
Pro Tips
- If you’re unsure where a specific node resides, use the Filter nodes input to highlight exactly what you need.
- The context menu (right-click on a node) gives you fast actions like color, delete, visibility toggle, and grouping options.
- Combine the Document View with the Inspector panel to both locate and modify molecular components easily.
Learning to use the Document View effectively can transform how you manage molecular models in SAMSON—especially in multi-component systems where clarity and control are essential.
To explore the full functionality of the Document View and related features, visit the SAMSON Interface documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.