For molecular modelers, one of the first challenges is getting started with your data. Whether you’re working with a protein data bank (PDB) file, molecular dynamics file, or other formats, loading and managing molecular structures efficiently can significantly affect your workflows. This blog post walks you through the essential steps and tips for opening local files and fetching structures seamlessly in SAMSON, the integrative molecular design platform.
Opening Local Files Made Easy
SAMSON provides an intuitive approach for loading molecular data from your computer. To open a local file, follow the path Home > File > Open, or simply press Ctrl + O on Windows/Linux or Cmd + O on Mac.
If you need to access recently opened files, navigate to Home > File > Recent to quickly pick from your history of documents. This feature is particularly handy when you’re juggling several projects or trying to revisit files you’ve recently worked on.
Smart Importers for Diverse File Formats
SAMSON supports multiple molecular file formats by leveraging specialized importers that recognize the file you open. By default, SAMSON includes importers for widely used formats such as PDB, mmCIF, and others. For an expanded library of importers, you can explore the SAMSON Marketplace, where additional tools and extensions are readily available.
Here’s a pro tip: the first time you use an importer, its default settings will be applied. However, SAMSON allows you to customize these parameters, which will then be saved for future use.
A good example is using the PDB importer. When importing a PDB file, you may need to specify options such as chain selection or additional adjustment parameters. With just a click on OK or pressing Enter, your file will load directly into SAMSON. Once loaded, you’ll see the molecular structure both in the Document view and in the main viewport, enabling efficient navigation and manipulation.
Fetching Files from Online Repositories
Need a molecular structure from the RCSB Protein Data Bank? SAMSON has you covered with the Fetch Structures tool. Simply follow Home > Fetch to download files in preferred formats such as PDB, mmCIF/PDBx, or MMTF. This integration can save you considerable time while working with commonly used protein and biomolecular data.
Extra Convenience with Multiple Documents
If you often work with different molecular systems simultaneously, SAMSON allows you to have several documents open at once. Only one document will be active at a time, visible in the Document view, but switching between them is effortless. Just go to Home > Documents or use the Documents list in the top-left corner of the interface to navigate between files.
This capability is especially useful when performing tasks such as comparing molecular structures, copying data between systems, or organizing components for large projects.
Next Steps: Turn Data into Discoveries
Once you’ve loaded your structures, a broad array of actions awaits you in SAMSON. You can proceed to Work with Structures for inspection and visualization tasks, or dive into Building Molecules for editing and construction.
Ready to explore more? Learn detailed instructions and advanced workflows in the full documentation available here.
SAMSON and all SAMSON Extensions are free for non-commercial use. Interested? Download SAMSON now at samson-connect.net.