As molecular modeling projects grow in complexity, so does the need to keep structures, simulations, scripts, and datasets well-organized. With multiple molecules, different simulation conditions, and embedded metadata, managing a project in a streamlined way isn’t just convenient—it’s essential.
If you’ve ever struggled to find a specific conformation, lost track of scripts used in previous runs, or wished you could bundle key components together for sharing or collaboration, folders in SAMSON documents might be exactly what you need.
What Are Folders in SAMSON?
In SAMSON, each document is a hierarchical structure composed of nodes, which can represent molecules, groups, cameras, scripts, data files, and more. Folders allow you to group any types of nodes together within a document. This helps you organize your work efficiently and makes it easier to perform batch operations, such as showing or hiding multiple molecules at once.
Why Use Folders?
Here are a few reasons why folders make molecular modeling in SAMSON more convenient:
- Group related molecules (e.g., ligands and receptors) for easy manipulation or visualization.
- Apply operations to an entire set (e.g., hide one category of molecules) with a single action.
- Encapsulate scripts or files related to specific parts of your project.
- Increase clarity when sharing the project with collaborators or moving between machines.
Creating and Using Folders
To create a new folder in your document:
- Click Edit > Folder from the top menu bar.
- Rename the folder to something meaningful (e.g., “Ligands_June2024”).
- Drag and drop the relevant nodes into the folder from the Document view.
Folders can be nested, renamed, moved, or deleted like any other node. This flexibility lets you structure your SAMSON document the same way you might arrange files and folders on your filesystem.
Embedded Files and Portability
One particularly useful feature of folders is the ability to embed files within them. Whether you’re working with supplemental data, supporting scripts, or annotated PDFs, these can all be stored directly within the document:
“Folders and files are stored within the document, making the document self-contained.”
This means you can transfer your entire project—including all references and context—to a colleague or another machine without any broken links or missing data.
Example: Organizing a Docking Study
Let’s say you’re performing a virtual screening study. You can:
- Create one folder for the protein structure and related preparation files.
- Create separate folders for each library of ligands tested.
- Add a folder for result analysis scripts and plots.
The result is an organized, shareable, and self-contained SAMSON document that offers clarity and control over even large-scale modeling efforts.
To learn more about how SAMSON handles documents, folders, and embedded content, visit the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.