When working with complex biomolecular systems, it’s easy to feel overwhelmed by the sheer number of atoms, residues, ligands, and other structural elements. Whether you’re modeling a protein-ligand interaction or preparing a system for simulation, one key challenge is staying organized within your modeling environment.
SAMSON offers a hierarchical Document view that addresses this challenge head-on, helping you gain clarity and control over your molecular systems. In this blog post, we explore how this powerful feature can streamline your molecular modeling workflow, especially when managing large or multi-component models.
What is the Document View?
The Document view is a hierarchical representation of your molecular system. It allows you to explore, select, organize, and manipulate the structure of your loaded models by visualizing nodes such as atoms, groups, molecules, folders, and more.
When Does It Help?
- You have opened multiple molecules and want to keep track of them easily.
- You need to group parts of the model, like solvent or ions, for better visibility or processing.
- You want to show or hide specific model components with precision.
- You are preparing a presentation and need to simplify the view.
- You want to quickly filter or find nodes matching specific criteria.
Key Features
- View the document’s structure: A clear tree-like hierarchy lets you navigate through molecules, atoms, and other node types.
- Filter nodes: Use the search bar to filter nodes by name or with the Node Specification Language (NSL) for advanced filtering.
- Reorganize structures: Easily drag and drop nodes to change how your project is organized.
- Context actions: Right-click a node to quickly apply actions like hiding/showing or colorizing directly from the document view.
- Multiple documents: Work with several molecular documents at the same time, switching between them using the Documents menu or keyboard shortcuts.
Selection Made Easier
Clicking on nodes within the Document view selects them in the viewport. This is incredibly useful when working with deeply buried atoms or complex compound assemblies where manual selection isn’t practical. The selection is fully synced: what you select in the Document view highlights in the structure, and vice versa.
Tips for Efficient Workflow
- Use Ctrl+1 (Windows/Linux) or Cmd+1 (Mac) to quickly toggle the Document view.
- Rename folders or structures with intuitive names to keep long sessions manageable.
- Use drag-and-drop to group related components (e.g., all water molecules or ligand fragments).
Conclusion
If you often find yourself losing track of components in large molecular systems, the Document view in SAMSON is an essential feature to explore. It provides a clear, interactive map of your project and helps you stay in control from beginning to end—whether you are preparing simulations, making visualizations, or analyzing molecular structures.
To learn more, visit the full SAMSON Interface documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.