Managing molecular models often means juggling multiple molecules, properties, and hierarchies within a single project. For many researchers and modelers, the challenge lies in keeping track of what’s loaded, what’s selected, or how different parts of a molecule are related. This is especially tricky when dealing with complex protein structures or comprehensive multi-molecule simulations.
Enter the Document View in SAMSON. 🎯 This often-overlooked feature simplifies how you see, organize, and interact with your molecular data. Let’s explore how it works—and why it might change the way you model.
What Is the Document View?
The Document View panel in SAMSON presents the hierarchical structure (or data graph) of the active document. It represents molecular structures in an intuitive tree format, making it easier to:
- Browse the entire model
- Select specific components
- Organize or reorganize structures
- Filter and visualize parts of the molecule
This tool becomes especially powerful when working with large assemblies, complex simulations, or comparative modeling involving multiple open documents.
Key Features You Might Like
- Easy Selection: Clicking in the Document View instantly selects atoms, residues, chains, or other structures, which are then highlighted in the viewport.
- Node Filtering: Use the filter bar to search by name or apply Node Specification Language (NSL) to smartly isolate node types.
- Quick Reorganization: Want to move components from one group to another? Just drag and drop in the tree.
- Context Actions: Right-click on any node for fast access to context-specific tools like hiding, visualizing, or labeling.
The Document View also integrates seamlessly with SAMSON’s familiar interface shortcuts. Access it via Interface > Document view or use the shortcuts:
- Windows/Linux: Ctrl + 1
- Mac: Cmd + 1
Multi-Document Navigation
Did you know SAMSON lets you open multiple documents at once? The Document View displays only the active document, but you can easily switch between documents using the Home menu or shortcuts:
- Ctrl / Cmd + Tab: Next document
- Ctrl / Cmd + Shift + Tab: Previous document
This is handy when you want to compare structures or transfer atoms between documents without manually saving and reopening files.
Use Cases
The Document View isn’t just navigation—it’s a tool to:
- Browse and modify molecular hierarchies for simulations
- Quickly identify ligands, ions, or residues of interest
- Prepare selections for visualizations or computational operations
- Track changes made during editing or simulations
If you’ve struggled to keep track of molecular fragments or manage selection groups in other software, spending time with SAMSON’s Document View will feel like a breath of fresh air. It brings clarity and control to your modeling workflow that scales with complexity, not against it.
Learn more directly in the SAMSON Interface Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.