Molecular modelers often juggle multiple structures, data sources, and editing operations all within a single session. As projects grow in size and complexity—especially in fields like drug discovery, protein engineering, or materials science—managing the structure and content of your workspace becomes crucial. That’s where Document view in SAMSON can make your work easier.
The Document view is not just a tree showing molecular objects. It gives you full control over your data hierarchy, node visibility, and even access to custom actions. If you’ve ever found yourself asking “what’s in this document again?” or hunting down a specific molecule among many, this feature is worth a closer look.
Why Does This Matter?
When you work with molecular simulations or build models from multiple experimental or predicted sources, things get messy fast. You might have several overlapping structures, annotations, simulation results, or notes in your SAMSON document. Document view helps you understand, search, and manipulate this content fast, saving you time and reducing errors.
What Can You Do with Document View?
- Browse the hierarchy of your document: Structures are shown in their nested organization (e.g., molecules inside folders, chains inside molecules, atoms inside residues).
- Search and filter nodes: Use the “Filter nodes…” search bar to find specific names or apply the Node Specification Language (NSL) to target nodes by type or property.
- Drag and drop: You can reorganize your structure by moving nodes around in the hierarchy.
- Batch actions: Right-click on nodes to access context menus for things like showing/hiding, deleting, grouping, labeling, and more.
- Select with precision: Selecting a node in the document view instantly selects it in the viewport (and vice versa), giving you tight coordination between data and visuals.
Working with Multiple Documents?
Document view becomes even more powerful when you’re working with multiple open documents. Each document has its own tree, and SAMSON shows the active one. You can quickly switch between documents via the Home menu’s “Documents” control or use keyboard shortcuts:
- Ctrl + Tab (or Cmd + Tab on macOS): Cycle through documents
This minimizes visual clutter and helps you isolate tasks like comparing ligand binding poses, editing animations for presentations, or preparing documents for sharing.
When Things Go Wrong: Undo & History
Let’s say you’ve accidentally deleted or moved a group of nodes while managing the document. You can bring up the History panel to undo changes and return to previous document states. This tight integration between Document view and History helps prevent data loss and experimental overhead.
Visual Example
This image displays a complete SAMSON document hierarchy, with molecules and their components clearly laid out. Nodes can be expanded, filtered, and acted upon directly here.
For more details and tips, visit the complete SAMSON Interface documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.