Managing complex molecular models—especially those involving large biomolecular systems, multiple ligands, or reference structures—can become overwhelming. Most molecular modelers have faced the frustration of cluttered data views, accidentally hiding key elements, or applying actions to unintended parts of a model.
One way to address this challenge when using SAMSON, the integrative molecular design platform, is by using folders in your molecular documents. Folders provide an efficient and robust way to group, manage, and apply actions to sets of nodes, such as proteins, ligands, solvents, or even scripts and conformation groups.
Why Organize with Folders?
Folders allow you to:
- Group related components together, like chains of a protein or ligands and cofactors.
- Quickly show or hide entire subsystems with a single click.
- Apply specific display styles or run scripts on predefined node groups.
- Keep exploratory structures separate from final models.
- Make documents easier to navigate and share with teammates.
Creating a Folder
In the SAMSON user interface, folders can be created directly from the menu bar:
Edit > Folder
This creates a new folder in your current document. You can then drag and drop any nodes—molecules, simulation elements, or other components—into the folder via the Document view.
Nested Organization
Folders can be nested, allowing for the creation of logical hierarchies. For example, you might organize a simulation as follows:
- System folder
- Protein
- Ligand
- Water box
- Reference States
- Scripts and Analysis
This kind of organization not only streamlines your workflow, but also makes collaborative work and document sharing more intuitive—everything stays in its place.
Embed Files into Folders
You can embed files (e.g. images, PDFs, data files) directly into folders. This is very useful when you want to include references, computational results, or even configuration files inside your document. These embedded elements make your SAMSON document fully self-contained and easy to transfer between systems.
Portable and Shareable
When you use folders and embed the necessary files, your SAMSON document becomes portable. This means:
- You can move it between computers or OSes without worrying about broken file paths.
- Your collaborators receive a complete, organized project they can open without configuration hassle.
These techniques are especially helpful during peer reviews, collaborative modeling projects, or when archiving computational work for future reference.
To learn more, visit the SAMSON documentation on documents and folders.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.