For molecular modelers starting out with SAMSON, one common challenge is efficiently loading molecular structures into the platform. Whether you are working with local files or fetching models from external databases, having a streamlined process is essential for productivity and focus on research. In this guide, we’ll walk you through the key methods for loading molecules into SAMSON and provide tips to enhance your workflow.
Opening Local Files
Loading a molecule from your local computer is intuitive. Simply navigate to Home > File > Open, or use the keyboard shortcut Ctrl + O (on Windows/Linux) or Cmd + O (on Mac). Once selected, SAMSON will automatically choose the appropriate importer based on the file format.
What’s great about SAMSON is that it supports a wide array of file formats by default. These include standard structure files like PDB, MMTF, and more. If you need even broader compatibility, explore the Marketplace on SAMSON Connect, which offers additional importers tailored to specific formats. Once your file is loaded, it will appear in the Document view and the viewport, ready for visualization or modification.
Additionally, if you need to revisit a file you’ve previously worked on, SAMSON makes it easy with its Home > File > Recent feature, which displays a list of recently opened files.
Fetching Structures from External Databases
Another powerful feature of SAMSON is the ability to fetch molecular structures directly from online databases such as the RCSB Protein Data Bank (PDB). To do this, use the Fetch Structures option, accessible via Home > Fetch. This tool lets you search and download files in popular formats like PDB, mmCIF/PDBx, or MMTF.
For researchers, this functionality can save hours of manual file downloading and reformatting. Simply search for the structure by its identifier or keywords, and SAMSON will handle the retrieval and formatting. The fetched structure integrates seamlessly into the Document view, ready for use.
Fine-Tuning Importer Parameters
When loading molecular files, different file types may come with specific parameters that need adjustment. For example, a PDB Importer dialog may appear, asking for additional input about how the file should be processed. SAMSON’s default settings are designed to provide optimal results initially. However, you can customize these parameters to suit your needs, and SAMSON will remember them for future imports.
This fine-tuning allows you to tailor the imported structures for specific workflows, ensuring greater flexibility and precision in your modeling tasks.
Seamless Workflow with the Document View
All loaded or created molecular files are centrally managed in the Document view. This is where SAMSON stores comprehensive information about your project, including atoms, bonds, molecules, models, and more. The Document view not only provides a data graph of your loaded structures, but also facilitates quick access to the active document.
For users juggling multiple projects, SAMSON allows you to have several documents open simultaneously, making it easy to switch between tasks without losing context. To switch documents, use the Documents list in the top-left corner of the menu, or follow Home > Documents. This capability can be particularly helpful when comparing different molecular structures or when copying segments from one document to another.
Next Steps
With molecules successfully loaded, think about your next steps. Do you want to edit your structure? Measure distances or angles? Or perhaps share the results with collaborators? SAMSON supports all these workflows and more.
To explore the full potential of SAMSON when it comes to handling molecular structures, visit the official documentation page for additional tips and resources.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at SAMSON Connect and take your molecular modeling to the next level.