Molecular modeling often involves working with deeply nested, multi-component structures, and navigating between different elements—residues, chains, ligands, or even different molecules—can become overwhelming. If you’ve ever found yourself hunting through a jumbled 3D scene or struggling to isolate a specific molecular chain, then it’s worth exploring a lesser-known but very useful feature in SAMSON: the Document view.
The Document view gives you a structured, hierarchical representation of everything in your active document. From a clean overview to precise selection and editing, it can streamline your work when dealing with large or complex models. It’s both a navigator and a control panel.
Why You Might Need It
Here are some common challenges molecular modelers face:
- Needing to isolate and export a specific ligand or subunit from a mixed system.
- Wanting to compare multiple models or mutant variants in the same scene.
- Cleaning up secondary components (like water or ions) before simulation prep.
- Simultaneously toggling visibility and selection across related groups of atoms.
The Document view lets you take control of these workflows in a visual and intuitive way.
What You Can Do With It
Once opened (Interface > Document view or Ctrl+1 on Windows/Linux, Cmd+1 on Mac), you’ll see a tree-style list of all nodes in your document, including models, groups, chains, residues, atoms, and more.
Use it to:
- Toggle visibility of individual nodes with a single click.
- Drag and drop nodes to reorganize your model hierarchy.
- Select anything—chains, ligands, atoms—directly from the list.
- Filter nodes interactively using names, labels, or Node Specification Language (NSL).
- Access context-specific actions from right-click menus.
This makes it much easier to work on specific subsystems without losing your place or disrupting the rest of your model.
Switching Between Documents
SAMSON allows multiple documents to be open at once—but only one is active. You can switch between them in several ways:
- Click the Documents list at the top of the SAMSON window.
- Go to Home > Documents.
- Use Ctrl+Tab to toggle forward (or Ctrl+Shift+Tab to toggle backward).
Each active document has its own Document view, helping you to clearly separate your different modeling tasks—whether you’re comparing structural variants or preparing systems for different simulations.
Visual Example
When a selection is made in the Document view, it’s instantly reflected in the 3D viewport, and vice versa. Filters and fine-grained visibility settings allow you to simplify your interface, especially when working on collaborative or publication-ready models.
Small Changes, Big Time Savings
Many SAMSON users overlook the Document view and rely solely on the 3D viewport. But as your projects grow in complexity, the time savings and clarity this feature offers become significant. It encourages a modular workflow—valuable if you’re working with large molecular assemblies, performing structure-based design, or preparing input for simulations.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.