As molecular modelers know, working on a single molecule is rarely the whole story. Often, you’re juggling multiple molecular systems, simulations, reference structures, and so on—each of which can quickly flood your workspace and leave you feeling lost. Have you ever found yourself wondering: “Which file contains that prepared structure for docking?” or “Where did I put that hydrophobicity annotation?”
Enter the Document View in SAMSON: a powerful yet underutilized tool that helps you visually navigate, organize, and interact with your molecular project’s structure.
What is the Document View?
The Document View in SAMSON displays the hierarchical structure of your active molecular document—nodes, models, annotations, folders, embedded files, and more. It’s like a molecular project outline that lets you stay in control.
Why Should You Use It?
Document View is especially useful when you’re dealing with complex projects involving:
- Multiple structures (e.g., protein-ligand systems, water boxes, ions)
- Prepared variants of the same molecule
- Embedded simulation data or files
- Annotations, notes, or visual styles you’d like to keep separate
Rather than navigating through the visual clutter in the viewport, you can edit and inspect everything using the document tree—quickly and precisely.
Top Features You Should Know About
- Show/Hide Control: Instantly toggle the visibility of any part of your model to focus only on what’s relevant.
- Drag-and-Drop Structure Rearrangement: Move nodes to reorganize your molecular data without touching your structures in the viewport.
- Context-sensitive Menus: Right-click any node to access tailored actions—like selection, labeling, or export options.
- Filtering: Use simple name filters or advanced queries with Node Specification Language (NSL) to find exactly what you need, even in large documents.
When to Use Document View Instead of the Viewport
Viewport interactions are great for visual inspection and interactive modeling. But Document View shines when:
- You want to batch show/hide specific atoms, residues, or folders
- You work on multiple molecules in one document and fear accidental changes
- You’re preparing structures for simulation or export and need fine-grained control
It also becomes essential when you have opened several documents: Document View reflects only the currently active document. Seamlessly switch between them using the Home > Documents menu or keyboard shortcuts (Ctrl+Tab or Cmd+Tab).
Getting Started
You can activate the Document View by clicking Interface > Document view, or using Ctrl+1 (Windows/Linux) or Cmd+1 (Mac).
Try docking a ligand, adding a few annotations, fetching a new protein from the database, and switching between document states—then open the Document View. You’ll see your modeling process in a whole new (and much clearer) light.
To learn more, visit the full documentation page: https://documentation.samson-connect.net/users/latest/interface/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.