For molecular modelers, one of the first steps in any project is loading structures into a molecular design platform. However, the process can sometimes feel daunting due to the variety of file formats and the need for flexibility in your workflow. SAMSON makes this process seamless, offering powerful tools to open, fetch, and embed structures within its ecosystem.
Opening Local Files
If you have molecular structures stored locally, SAMSON provides several methods to load them efficiently. To open a file, navigate to Home > File > Open or use the shortcut Ctrl + O on Windows/Linux and Cmd + O on macOS. For recently opened files, you can access them through Home > File > Recent, saving you time when revisiting previous projects.
Behind the scenes, SAMSON uses specialized importers to handle various formats. By default, SAMSON supports multiple file types, from PDB to MMTF, but additional importers can be acquired via the Marketplace on SAMSON Connect. This flexibility ensures that your specific file format is never a barrier to getting started.
Fetching Structures Online
Molecular modelers often rely on online repositories such as the RCSB Protein Data Bank. SAMSON simplifies this process with the Fetch Structures tool, accessible via Home > Fetch. With this feature, you can fetch files in various formats like PDB, mmCIF/PDBx, or MMTF and start working on them immediately. Whether you’re modeling proteins, complexes, or other macromolecules, fetching online structures is just a few clicks away.
Embedding Files for Maximum Portability
Say goodbye to disconnected data files spread across folders. SAMSON introduces a unique feature: Universal File Embedding. You can embed Python scripts, research papers, images, or supplementary data directly into a SAMSON document. Simply drag and drop your files or folders into SAMSON, and you’ll be prompted to embed them. Alternatively, use Home > Embed files or Home > Embed folders.
This embedding capability makes your documents self-contained. Sharing data becomes more convenient, and transferring projects between computers ensures nothing gets left behind. Whether you’re running machine learning tasks with embedded Python scripts or sharing a fully self-contained project, SAMSON provides a streamlined workflow for collaboration and portability.
Tips for Beginners
If you’re new to SAMSON, consider starting with basic tasks like loading structures before diving into advanced workflows. Use the Document view to see loaded data, which provides insights into the active document, spanning atoms, bonds, molecules, models, and more. Want to work on multiple structures simultaneously? Open several documents and switch between them effortlessly via Home > Documents.
To explore the many ways you can extend SAMSON’s functionality, visit the Marketplace on SAMSON Connect, where you can download additional apps and extensions tailored to your specific molecular design needs.
Now that you understand how to load molecules, why not take the next steps? Explore editing and simulation workflows, share your projects, or dive into collaborative features, all within SAMSON.
For more detailed instructions and examples, visit the official documentation page: https://documentation.samson-connect.net/users/latest/loading-molecules/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at https://www.samson-connect.net.