As molecular modeling projects grow in complexity, keeping everything organized—especially when dealing with multiple structures, simulations, and annotations—can become a real challenge. Mistakenly overwriting an important molecule, struggling to recall how a selection was made, or navigating through scattered files are all-too-familiar frustrations for many molecular modelers.
If this sounds familiar, the Document View in the SAMSON molecular design platform might become your favorite feature. Let’s explore how this underused interface panel can help you take control of your molecular data, streamline your workflow, and stay focused on design and analysis rather than housekeeping.
What is the Document View?
The Document View presents a hierarchical data graph of the active document, visualizing all its components—molecules, atoms, folders, annotations, simulations, renderings, and more. Whether you’re building a protein-ligand complex or visualizing a reaction path, the Document View gives you a clear overview of your entire system.
Why Does This Matter?
As a molecular modeler, your document may contain:
- Multiple imported structures (e.g., proteins and ligands)
- Generated visualizations and analysis outputs
- Python scripts, notes, or folders for organization
- Simulation states and results
Without a proper overview, losing track of specific entities—or worse, making unintended changes—becomes very easy. The Document View minimizes that risk by treating your molecular project like a structured tree.
Key Features That Improve Your Workflow
- Show/Hide Nodes: Instantly control visibility without deleting anything.
- Selection Sync: Selecting an object in the Document View highlights it in the viewport—and vice versa.
- Filtering: Use Node Specification Language (NSL) expressions or simple names to find exactly what you need. It’s like a search engine for your document.
- Reorganize on the Fly: You can drag and drop nodes to restructure your file. For instance, move all ligands into a single folder for batch visualization or export.
- Context Menus: Right-click any node to run specialized actions relevant to its type—for example, isolate a selection, apply coloring, or export it separately.
Working With Multiple Documents? No Problem.
Have several molecular systems you’re working on at once? SAMSON allows opening multiple documents simultaneously. You can switch between them via:
- The Documents list in the top-left corner
- Home > Documents in the ribbon menu
- Shortcuts:
Ctrl+TaborCmd+Tab(and Shift versions)
This makes it simple to transfer data between documents or work in specialized environments for different stages of your modeling workflow.
The Takeaway
If your SAMSON document feels like a black box, the Document View is the light switch. It helps you gain a deeper understanding of your file’s structure and ensures you stay productive and in control, especially as your projects grow.
To learn more and explore the full potential of the SAMSON interface, visit the official documentation page: 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.