Making Sense of Molecular Hierarchies with SAMSON’s Document View

When working on complex molecular modeling projects, it’s easy to feel overwhelmed by the growing number of molecular structures, edits, and simulation elements. Proteins, ligands, solvents, surfaces, cameras, animations—everything piles up, and soon you’re asking: where did I put this structure? What atoms did I prepare? How can I isolate just the part I’m interested in?

Enter the Document View in SAMSON, a feature that simplifies the chaos by showing you a complete, searchable, interactive hierarchy of your document’s molecular content. Whether you are designing, analyzing, or simulating molecules, understanding and navigating this structure can save you time and help you avoid costly mistakes.

What is the Document View?

The Document View presents a hierarchical graph of your currently active SAMSON document. Think of it as a file explorer—only for your molecular system.

The document view shows a structure of a SAMSON document

Within this view, you can:

  • Inspect the full structural breakdown of your document—from molecules and residues to atoms and bonds.
  • Toggle the visibility of individual nodes or groups of nodes.
  • Select and manipulate nodes, such as fitting a protein chain, changing visualization, or copying parts between documents.
  • Use advanced filters based on the Node Specification Language or node names to find exactly what you need.

Why This Matters

This hierarchical overview is especially helpful when dealing with structures fetched from public databases (like RCSB or AlphaFold) that often contain multiple chains, ligands, solvent molecules, or ions. Rather than browsing through them inside the 3D viewport, you can quickly locate and modify nodes directly in the Document View.

Copying parts of molecules, comparing structures across open documents, and organizing simulation inputs becomes much more manageable when you can see everything laid out logically.

How to Access the Document View

You can open the Document View by navigating to:

Interface > Document view

Or press:

  • Ctrl + 1 on Windows/Linux
  • Cmd + 1 on macOS

You can switch between multiple open documents using the top-left menu or Home > Documents.

Switching between documents

Tips for Smarter Navigation

  • Drag-and-drop nodes to reorganize the structure of your document.
  • Right-click any node to access specialized actions, like creating a visual model or applying presets.
  • Use filters to locate nodes by name or attributes—for example, find all water molecules or a specific ligand quickly.
  • Select nodes in the view to highlight them in the viewport. This makes operations like alignment, coloring, or measuring far more efficient.

Selecting nodes in the document view

The Document View is something many users don’t fully explore at first, but once you do, it becomes one of those tools you don’t want to live without. Cleaner projects, faster workflows, and fewer selection mistakes—these are small wins that add up.

To learn more about the SAMSON interface and Document View, visit the original documentation page.

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

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