One persistent challenge for molecular modelers is managing and organizing complex structural data. Whether you’re working with molecules, scripts, conformations, or files, keeping track of this information in an efficient manner can significantly impact your productivity. SAMSON offers a solution: the powerful Document view. If you’ve struggled with structuring your molecular data, let’s explore how SAMSON’s document organization tools can help simplify your workflow.
Understanding the Document Structure
SAMSON documents are hierarchical storage containers where various elements—such as molecules, residues, atoms, Python scripts, and cameras—are stored as nodes. These nodes form a tree-like structure that captures all aspects of your molecular project. Each document represents a unique data graph, and you can view this in the Document view panel.
In fact, the Document view is one of SAMSON’s most efficient features. It opens up the ability to:
- Explore the structure of your project hierarchy
- Show or hide individual nodes
- Select specific nodes efficiently
- Filter nodes using the Node Specification Language
- Organize your nodes by dragging and dropping them
- Apply contextual actions quickly using the toolbar
By visualizing your molecular data this way, you not only gain better oversight but also improve the accessibility of key project components.
Managing Multiple Documents
Molecular projects can vary in size and complexity. SAMSON allows you to open multiple documents simultaneously, although only one of them is active at a time. Switching between these documents is intuitive: simply use the Documents list in the top-left corner of the SAMSON interface. This feature is a lifesaver when working on related tasks involving different molecules or when you need to copy nodes across projects. The ability to manage multiple documents seamlessly can help streamline your productivity and focus.
For users who often return to ongoing projects, the Home > File > Recent option ensures recently used files are always at your fingertips. Additionally, creating new documents is straightforward—just follow Home > File > New.
Embedding Folders and Files
A standout feature of SAMSON documents is their ability to embed folders and files within the document itself. You can attach PDFs, structure files, scripts, datasets, images—virtually any file type—directly into the project. This ensures the document remains self-contained, making it sharable and portable across devices without losing the supporting data. To take this further, SAMSON’s folder system helps you group elements. This way, you can apply actions to entire sets of nodes, such as showing or hiding multiple molecules with a single click.
For example, consider an instance where you’re modeling a large biomolecule system with multiple ligands and conformations. You can group these ligands into folders, filter them using names or attributes, and visualize them in selected combinations. This organization isn’t just for convenience—it can enhance how you analyze and communicate your findings.
Get Started with the Document View
Ready to explore this feature? Open the Document view panel by selecting Interface > Document view. Alternatively, use the shortcut Ctrl+1 (Windows/Linux) or Cmd+1 (Mac). Once your Document view is visible, the hierarchical data graph will help you navigate, filter, and organize the nodes with ease.
To learn more about SAMSON’s document management features, including embedding files and setting up folders, visit the full SAMSON documentation on documents. Dive into a new era of organization and take control of your molecular modeling data!
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON for free at SAMSON Connect.