A Simple Way to Stay Organized When Modeling Molecules

If you’ve worked on large or multi-step molecular modeling projects, you’ve probably faced the challenge of managing complex structures, reference files, scripts, and various annotations — all within a single workspace. Managing molecular data can quickly become overwhelming when everything is scattered in different folders or files. Fortunately, SAMSON offers a clean and efficient solution through its Document view.

Documents in SAMSON act as centralized containers for all of your modeling data. Think of a Document like a smart project folder: it holds molecules, atoms, groups, conformations, scripts, images, PDFs — virtually any file you may use during molecular modeling. And you can open several documents at once, easily switching between them or even copying molecular structures from one to another.

What is the Document View?

The Document view visually represents the internal structure of your document as a hierarchical data graph. You can access it from the top bar via Interface > Document view, or by using the shortcut:

  • Ctrl + 1 on Windows and Linux
  • Cmd + 1 on Mac

The document view shows SAMSON document structure

Why This Matters

Molecular modeling often involves keeping track of multiple entities. You may want to simulate the interactions of different molecules, compare conformations, embed scripts for specific analysis workflows, or annotate structures for later reference. If your workspace is cluttered or if your files are scattered across directories, mistakes can happen — or worse, time is lost.

With the Document view, you can:

  • View and navigate the hierarchical structure of the project
  • Show/hide nodes as you need them
  • Select nodes or groups of nodes efficiently
  • Filter nodes by name or using the Node Specification Language
  • Drag and drop nodes to restructure your data graph
  • Apply specialized actions to nodes via contextual menus

This is especially helpful when managing simulations with multiple molecules, navigating between different versions of a structure, or performing scripting and automation workflows.

Managing Multiple Documents

You can open multiple documents simultaneously and switch between them using the Documents dropdown in the top-left corner or via:

  • Ctrl + Tab and Ctrl + Shift + Tab on Windows
  • Cmd + Tab and Cmd + Shift + Tab on macOS

Switching between documents

This feature is useful if you’re working on several stages of a project—for example, comparing docking results across different proteins, or preparing a publication and keeping visualization-ready versions of structures separate from raw data.

Getting Started

To create a new document, go to Home > File > New or use the shortcut:

  • Ctrl + N on Windows and Linux
  • Cmd + N on macOS

You can also open recently edited documents through Home > File > Recent.

Conclusion

Leveraging the Document view in SAMSON allows you to stay organized, reduce errors, and streamline your molecular modeling workflows. Whether you’re analyzing multiple molecules or integrating scripting and embedded resources, this tool helps keep everything accessible in one place.

To learn more, visit the full documentation at https://documentation.samson-connect.net/users/latest/documents/.

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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