Working with complex molecular systems involves not just visualization, but also managing the structure of the data. For molecular modelers, this can quickly become a challenge—especially when handling large protein assemblies, predictions from AlphaFold or Chai-1, or multiple working hypotheses stored in parallel.
That’s where SAMSON’s Document View comes in. If you’ve ever wished for a more transparent way to see and manage your molecular scene, this feature can save you time and reduce mistakes.
What is the Document View?
The Document View displays the hierarchical data graph of the active SAMSON document. Each node represents an object in the scene, such as atoms, residues, molecules, folders, notes, or even Python scripts.
This gives you full control of the molecular objects you’re working with, and makes it easier to manage very large systems.
Why does this matter?
- Navigation: Drastically improves browsing through large biomolecules, nanostructures, or supramolecular assemblies.
- Troubleshooting: See hidden, overlapping, or unintended elements that might cause simulation or rendering issues.
- Selection: Select precisely the parts you want to simulate, export, or visualize using node names or patterns.
- Organization: Add folders, notes, or group elements logically to keep your project accessible and clear for collaborators—or your future self.
Main Features
- Show/hide nodes without removing them
- Filter by name or by Node Specification Language
- Drag-and-drop reorganization for tidy results
- Context menus for fast access to visual presets, simulation tools, or editors
Working with Multiple Documents
SAMSON allows multiple documents to be opened simultaneously. Each document appears in the Document View when active, allowing you to copy between them or work in parallel on different hypotheses. To switch between documents, simply use:
- Home > Documents menu
- or
Ctrl + Tab/Cmd + Tabshortcut
Examples in Practice
Imagine importing a protein structure from RCSB and embedding trajectory data, ligands, and calculation results from AlphaFold. With the Document View, you can:
- Group residue chains for better overviews
- Hide water molecules temporarily from the graph
- Tag and annotate key residues or domains
- Quickly notice any duplicated or incomplete entries
This clarity makes it easier to publish, share, simulate, or extend molecular models responsibly.
To learn more about the Document View and other interface components, visit the official SAMSON Interface Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.