As your molecular models grow bigger and more complex, staying organized becomes essential. Whether you’re aligning protein structures, preparing ligands, or scripting simulations, you’re likely juggling multiple structures, tools, and settings at once. This is especially true when working on multidomain proteins or hybrid systems combining nucleic acids, ligands, and ions. What if you could get a complete view of your system, including all its components and operations, at a glance?
The Document view in SAMSON provides exactly that: a tree-like hierarchical view of your current molecular document, where you can easily manage structures, attributes, scripts, and more.
Why the Document View Can Make Your Work Easier
Think of the Document view as a control panel for your model. It gives you the ability to:
- Visualize the structure of your molecular model as a data graph
- Filter nodes by name or type—very handy for large systems
- Show or hide nodes without affecting the whole document
- Organize nodes by drag-and-drop (managing folders, selections, groups)
- Quickly select structural elements based on hierarchy
If you’ve ever needed to isolate a ligand and its interacting residues in a protein target or examine chain-level representations in a macromolecule, you’ll appreciate the precision this view allows.
Live Selection and Filtering
You can select nodes directly from the Document view. That means you can activate, analyze, or apply commands only to those selected parts. Use the Filter nodes… field to find specific residues, chains, or objects. The Node Specification Language is supported, making advanced queries (e.g., all hydrophobic residues in chain A) possible.
Switch Between Multiple Molecular Documents
Many molecular modeling workflows involve comparing or combining molecules—e.g., docking ligands into successive protein conformations, or preparing multiple solvated systems. The Document view allows you to have several documents open at once and easily switch between them.
To switch between documents, you can:
- Click on the Documents list in the top-left corner
- Select Home > Documents
- Use the
Ctrl + TaborCmd + Tabshortcuts (and addShiftto reverse)
Accessing the Document View
You can open the Document view by navigating to Interface > Document view or using the following shortcut:
- Windows/Linux:
Ctrl + 1 - Mac:
Cmd + 1
This view is especially useful when combined with the Inspector panel (to edit selected node properties) and the Python Console (for scripting localized operations within selections).
Whether you’re preparing simulations or curating structural data, the Document View will help you stay organized and increase modeling efficiency. Learn more.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.