When working on complex molecular modeling projects, juggling multiple molecules, simulations, scripts, and views can quickly become overwhelming. A common pain among molecular modelers is managing large projects that involve many interconnected parts. Small mistakes in organization can lead to confusion, lost time, or even data loss. If this sounds familiar, SAMSON’s Document system might be the solution you didn’t know you needed.
A SAMSON Document serves as a container for managing everything related to your modeling project: from molecules and conformations to scripts and even embedded files like PDFs or images. Think of it as your project’s digital notebook – structured, accessible, and versatile.
Why documents matter
Instead of storing your molecules separately and switching between them through file explorers, SAMSON lets you open multiple documents in the same session. You can have different molecular systems in parallel – for example, a ligand in one document and a protein structure in another. You can copy or compare structures across documents easily.
At any time, only one document is active: that’s the one shown in the Document view. You can quickly switch between open documents through the dropdown in the top-left corner or use keyboard shortcuts like Ctrl + Tab (on Windows/Linux) or Cmd + Tab (on macOS).
Folders: your structure’s best friend
Documents can contain Folders, allowing you to group nodes logically. For instance, you can place all ligands into one folder, water molecules in another, and scripts in yet another. This helps you:
- quickly show/hide related sets of molecules,
- apply actions like transformations or color changes to an entire group,
- maintain a tidy workspace as your project grows.
To create a folder within a document, use Edit > Folder, or press Ctrl + Shift + F (Windows/Linux) or Cmd + Shift + F (Mac).
One powerful feature: folders are embedded within the document along with the contained data. You can store structure files, images, CSV files with results, or even Python scripts directly inside a document. This ensures that your project becomes self-contained, making it easy to move between computers or share with collaborators.
Getting started with documents
Creating a new document is simple: navigate to Home > File > New or use the shortcut Ctrl + N / Cmd + N. For recently used projects, you can reopen documents via Home > File > Recent.
All these features make the SAMSON document architecture especially powerful for large-scale molecular design. Whether you’re modeling a single molecule or working on multi-system simulations, using documents and folders saves time and keeps your workflow clean.
To learn more, visit the full documentation on SAMSON Documents.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.