Stop Getting Lost in Molecular Models: How Document View Helps You Stay Organized in SAMSON

Molecular modelers often juggle multiple structures, simulations, and scripts all at once. Keeping track of everything inside a complex molecular modeling project can quickly become overwhelming—especially when dealing with large biomolecular systems or comparing multiple candidate structures. That’s where the Document View in SAMSON comes in.

Whether you’re analyzing a protein-ligand complex, building small molecules, or running simulations, SAMSON’s Document View offers a visual, hierarchical overview of your project, making it easier to organize, manage, and interact with molecular data.

What is the Document View?

The Document View displays the hierarchical structure of your active SAMSON document. Molecular systems are represented as a tree-like data graph where atoms, residues, chains, molecules, and more are structured in a parent-child relationship. If you’re working with multiple systems, you can easily switch between them, manage selections, and drag-and-drop to reorganize.

The document view shows a structure of a SAMSON document

Why Is This Useful?

Here are a few practical reasons molecular modelers use Document View every day:

  • See what’s in your document: Get a quick overview of everything you’re working on—from individual atoms to full systems.
  • Hide or show components easily: Toggle visibility for selected groups to focus only on relevant parts.
  • Reorganize structures intuitively: Drag nodes to re-root parts of your structure graph and group/edit them accordingly.
  • Filter using powerful queries: Use the built-in filter to search nodes by name or through the Node Specification Language (NSL).
  • Multi-document support: Switch between documents when handling multiple systems or preparing comparative studies.

Quick Actions in the Document View

Each node has an associated context menu and toolbar that lets you:

  • Select/Deselect parts of the model
  • Apply actions (e.g., delete, label, visualize)
  • Use selection tools based on properties (e.g., select by residue names, chains, types of atoms)

These actions act directly in context—helping you avoid distractions and keep your workflow smooth.

Working With Multiple Documents

Another underestimated feature: SAMSON supports multiple open documents. Only one is active at a time, but switching is as simple as using interface buttons or the shortcuts Ctrl + Tab and Ctrl + Shift + Tab (on Windows/Linux), or Cmd equivalents on macOS.

Switching between documents

How To Open the Document View

You can open it through:

  • Interface > Document View
  • Shortcut: Ctrl + 1 (Windows/Linux), or Cmd + 1 (Mac)

Real-World Tip

Before beginning any visualization or simulation, spend a minute in the Document View to clean up and rename parts of your structure. It’ll make downstream analysis (e.g., measurements, animations, sequence alignments) much easier and more readable.

Learn More

To dive deeper into what you can do with the Document View, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/interface/.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.

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