Molecular modelers often work on multiple structures simultaneously—preparing systems, analyzing interactions, or designing new molecules. But managing these workflows effectively can be challenging. You might find yourself juggling several PDBs and simulations, switching back and forth between them to cross-reference or transfer information. SAMSON provides a simple, intuitive system to manage and switch between multiple open molecular documents, solving a common productivity pain point.
In this blog post, we’ll explore how the interface in SAMSON allows easy access to multiple projects, reducing the need for repetitive file opening and closing, and helping you stay focused on your research.
Opening and Navigating Between Documents
SAMSON lets you keep several molecular documents open at once. Each document represents a distinct molecular system or project. You can switch seamlessly between them in a few clicks.
To manage and switch open documents, use the Home > Documents group in the ribbon menu. It includes a counter showing how many documents are currently open and a dropdown menu to toggle between them.
You can also use useful keyboard shortcuts:
- Ctrl + Tab (or Cmd + Tab on Mac): Switch to the next document.
- Ctrl + Shift + Tab (or Cmd + Shift + Tab): Switch to the previous document.
Here’s how the document selection interface looks:
Viewing Current Document Structure: Document View
Each document contains a hierarchical structure of molecular nodes, including atoms, bonds, residues, and groups. You can visualize and interact with this structure using the Document view.
To open the Document view, go to Interface > Document view or press Ctrl + 1 (Cmd + 1 on Mac).
Features of the Document view include:
- Exploring the molecule’s hierarchical structure
- Hiding/showing nodes
- Selecting parts of the structure using filters or search
- Dragging nodes to change the structure
- Using right-click context menus for quick actions
When and Why This Is Useful
Suppose you’re comparing a ligand binding pose in multiple protein structures, or extracting fragments from an existing library to design a new compound. Instead of reloading files one by one, you can have all the relevant files open and switch between them instantly.
With the document view, you gain more control over what parts of your system are active or visible, aiding both clarity and performance. And if you’re writing scripts or preparing presentations involving multiple molecules, this workflow becomes even more essential.
Conclusion
Becoming fluent in SAMSON’s document management tools can greatly enhance your modeling workflow, especially when juggling multiple structures or simulations. Keep your data organized, reduce redundant file operations, and make better use of SAMSON’s integrated design and modeling capabilities.
To learn more about SAMSON’s user interface and features, visit the full documentation page: https://documentation.samson-connect.net/users/latest/interface/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.