If you’ve just started with SAMSON, the integrative molecular design platform, one of the first tasks you’ll need to tackle is loading molecules. Whether you’re working with local files, fetching molecular structures, or integrating project materials, understanding how to bring data into SAMSON effectively is essential. This guide will help you navigate the process, ensuring your workflow starts on the right track.
Using Local Files and Fetching Structures
Loading your first molecular structure in SAMSON is straightforward, thanks to the platform’s intuitive interface and extensive format support. To open a molecule from a local file, you can follow this simple path:
Home > File > Open.
For those who enjoy using keyboard shortcuts, you can press Ctrl + O on Windows/Linux or Cmd + O on Mac. If you’ve recently worked on a file, you’ll find it conveniently listed under Home > File > Recent.
But what happens if the file format requires a specific importer? SAMSON intelligently selects the appropriate importer for the format you are working with. By default, SAMSON supports a variety of molecular formats, such as PDB, mmCIF, MMTF, and more (see the full list here). If additional capabilities are required, you can explore more importers on the SAMSON Connect Marketplace.
Tip: When using an importer for the first time, you may be prompted to specify additional parameters. These settings are saved after the first use, streamlining subsequent workflows. For example, working with PDB files might involve specifying chain selections or resolution settings—check the screenshot below for a preview:
Once your parameters are in place, click OK or press Enter, and your structure will appear in SAMSON’s interface, including the Document View and the central viewport.
Fetching Data from Online Resources
Another powerful feature is SAMSON’s integration with online databases. Using apps such as Fetch Structures (accessible via Home > Fetch), you can conveniently download data from the RCSB Protein Data Bank. Supported formats include PDB, mmCIF/PDBx, and MMTF, enabling researchers to explore a rich library of molecular data without ever leaving the platform.
A Versatile Document Framework
When you load or create molecular structures, they’re stored within SAMSON’s active document. This document is your workspace, where all atoms, bonds, molecules, simulators, and enhancements are stored in a structured data graph.
Curiously, SAMSON allows you to keep multiple documents open simultaneously, allowing for greater flexibility in managing projects. For instance, you can analyze different molecules in isolation or transfer segments between documents. Switching between active documents is as easy as accessing the Documents list via the menu or pressing quick shortcut keys.
Need to start fresh? Create a new document with Home > File > New or Ctrl + N/Cmd + N. Revisiting recent work? Go to Home > File > Recent for immediate access.
Want to Learn More?
These features make SAMSON a uniquely versatile tool for molecular modelers, simplifying the process of working with diverse data types and preparing projects for advanced workflows such as visualization or simulation. To delve further into importing files, fetching structures, and managing documents, visit the official documentation at https://documentation.samson-connect.net/users/latest/loading-molecules/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Start exploring by downloading the platform here: https://www.samson-connect.net.