Working on complex molecular systems often means managing numerous components: multiple protein structures, ligands, solvents, ions, and various annotations or scripts. This complexity can quickly become overwhelming, especially when switching between tasks or sharing projects across teams.
This is where SAMSON’s Document View becomes a quiet but powerful ally. If you’re not already using it to manage your molecular projects, you’re likely spending more time than necessary navigating and organizing your models.
What is the Document View?
The Document View displays the hierarchical data graph of your current SAMSON document. Think of it as a tree view of everything in your molecular scene — from entire structures down to individual atoms. It allows you to navigate, organize, and access your data in a visual and structured way.
Why It Matters
Imagine you’re modeling a multimeric protein and want to align a specific chain from one monomer to another. Without a structured view, selecting the right chain might involve clicking through crowded visuals or relying on guesswork-based naming. With Document View, you can drill down precisely and quickly, hide what you don’t need, and focus on key parts of the system.
Key Benefits
- Clear Structural Overview: Get a complete picture of all molecular components organized in a logical tree.
- Quick Selection and Filtering: Select nodes directly and apply custom filters using the Node Specification Language (NSL) or by name.
- Drag-and-Drop Organization: Easily restructure molecules, reparent nodes, or combine parts into groups by dragging them in the hierarchy.
- Contextual Actions: Right-click any node to access relevant actions like visualization presets, property modifications, or even deleting unnecessary elements.
Working with Multiple Documents
SAMSON allows you to have multiple documents open simultaneously — useful when comparing structures or transferring pieces between models. The Document View reflects the active document, and you can switch using the Documents menu or keyboard shortcuts like Ctrl/Cmd + Tab.
Tips for Better Workflow
- Frequent Save-Selection-As: Use the document view to select only key nodes and export them cleanly using Save selection as….
- Naming Conventions: Rename nodes meaningfully for quick identification from the hierarchy.
- Use Notes and Scripts: Right-click and add notes or Python scripts directly to manage chunks of logic or commentary ideas tied to specific structures.
Access and Shortcuts
You can open the Document View via Interface > Document view or by using the shortcut Ctrl/Cmd + 1.
The Document View is an underused but essential part of a more controlled and efficient modeling workflow, especially when projects grow in size and complexity.
To learn more about the interface, visit the SAMSON Interface documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.