Keeping track of complex molecular models can be a challenge, especially when working with large biomolecular systems or managing multiple simulation setups. Whether you’re designing a drug candidate, investigating protein-ligand interactions, or comparing molecular structures, having a clear overview and streamlined control over your workspace can save hours of frustration.
This is where the Document View in SAMSON comes in. It gives you an interactive map of your model’s structural hierarchy — turning a cluttered molecular scene into an organized and navigable interface.
What Is the Document View?
The Document View shows the hierarchical structure of the active document in SAMSON. Think of it as the file explorer of your molecular document — each node representing atoms, residues, chains, visual models, annotations, and more.
Once opened, the Document View allows you to:
- Visually browse through the components of your molecular system
- Instantly filter, select, and manipulate groups of atoms or molecules
- Reorganize parts of the document through drag-and-drop
- Toggle visibility of nodes (e.g., only show a ligand or hide water molecules)
- Use powerful filtering with the Node Specification Language (NSL)
When Does It Help?
If you’re working with multiple chains, ligands, or simulation results, it can be tedious to switch back and forth between selections and configurations. The Document View streamlines those interactions.
Examples of situations where the Document View saves time:
- Quickly selecting all ligands or hiding water molecules by name or type
- Copying structures from one document to another via drag-and-drop
- Filtering nodes with specific tags or structure IDs
- Locating prepared visual elements like cameras or lights
It becomes especially useful when you’re preparing figures, automating tasks via scripts, or debugging a complex setup (e.g., modeling simulations with multiple systems open).
How to Open and Use It
To open the Document View, click:
- Interface > Document view
Or use:
- Ctrl + 1 on Windows/Linux
- Cmd + 1 on Mac
You can navigate the hierarchy with ease, expand/collapse branches, right-click nodes for actions, or apply rich filters that help isolate exactly what you’re looking for.
Here’s how it looks in action:
Working with Multiple Documents
SAMSON allows you to open multiple documents simultaneously. You can switch between them via:
- Home > Documents dropdown
- Ctrl/Cmd + Tab (next)
- Ctrl/Cmd + Shift + Tab (previous)
Only one document is active at any time — the one shown in the Document View.
Conclusion
The Document View is more than a panel — it’s a control center for molecular modelers who want clarity and control over complex systems. Whether you’re selectively hiding details for a cleaner visualization or quickly navigating large biosystems, this feature reduces cognitive load and improves workflow fluency.
Learn more about the SAMSON interface and how to make the most of your modeling sessions.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.