Working with Multiple Molecular Documents Simultaneously

When working on complex molecular modeling projects, there’s often a need to open and compare several molecular structures, run different types of simulations, or organize exploratory paths independently. For researchers using SAMSON, knowing how to work efficiently with multiple documents is key to improving clarity and productivity.

What is a Document in SAMSON?

In SAMSON, a document is a container that holds all data related to a modeling session: atoms, bonds, molecules, models, simulations, scripts, and even embedded files. Each document is visualized via the Document view, which allows users to navigate and manage complex data graphs representing their molecular systems.

One Active Document at a Time

While you can open multiple documents simultaneously in SAMSON, only one document is active at a time—the one shown in the Document view. This design helps prevent confusion, especially in workflows that involve editing or simulating different molecules separately.

Switching between documents is straightforward:

  • Click the Documents list in the top-left corner of the SAMSON interface
  • Or navigate via Home > Documents

Alternatively, you can use keyboard shortcuts:

  • Windows/Linux: Ctrl + Tab and Ctrl + Shift + Tab
  • Mac: Cmd + Tab and Cmd + Shift + Tab

Switching between documents

Creating New Documents

You can easily create new documents using:

  • Home > File > New
  • Or use the shortcut: Ctrl + N (Windows/Linux) or Cmd + N (Mac)

This is particularly useful when you want to copy-paste parts of molecular systems between documents or work on parallel modeling tasks without mixing data.

Working Smarter: Why Multiple Documents Matter

Here are a few scenarios where leveraging multiple documents can reduce complexity and help avoid mistakes:

  • Comparative modeling: Load homologous structures in separate documents to emphasize structural differences without interrupting analysis pipelines.
  • Simulations and preparation: Run a simulation in one document while preparing a modified molecular version in another.
  • Script testing: Test Python scripts on small datasets in a temporary document without affecting your main modeling setup.

In all cases, organizing molecular content across documents can make your SAMSON workspace more focused and modular, decrease clutter, and reduce the likelihood of editing the wrong structure or model.

Learn More

To dive deeper into managing documents in SAMSON, consult the original documentation page at this link.

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

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