As a molecular modeler, one of the first challenges after installing a molecular design platform like SAMSON is loading the files you need to work on. Whether you’re opening molecular structures stored locally, importing project files, or fetching structures directly from the Protein Data Bank (PDB), knowing how to navigate the loading process can save you time and streamline your workflows.
This guide will take you through the practical steps for loading molecules into SAMSON, ensuring you can focus on your scientific exploration rather than technical hurdles.
Opening Local Files
SAMSON offers two main ways to open local molecules:
- Home > File > Open
- Keyboard shortcuts:
- Windows/Linux:
Ctrl + O - Mac:
Cmd + O
If you’ve recently worked on a document, you can quickly access it via the Home > File > Recent menu.
When you load a structure, SAMSON automatically identifies and applies the appropriate importer based on the file format. Supported formats include popular ones like PDB, mmCIF, and MMTF. Check the list of supported formats for more details.
Specifying Import Parameters
Many importers let you customize parameters during the loading process. For example, when importing PDB files, you may encounter dialog windows that allow you to adjust specific settings:
Once the parameters are set, they are saved for future imports, ensuring consistency in your work.
Fetching Structures from Online Databases
In addition to loading local files, SAMSON enables you to fetch molecular structures directly from the RCSB Protein Data Bank. This is achieved through the Home > Fetch feature or specific third-party Apps. Supported formats for fetched files include PDB, mmCIF, and MMTF — ensuring compatibility with widely used databases.
Keeping Documents Organized
Once your molecular structure is loaded, it becomes part of a SAMSON document. The Document view helps you manage and visualize all loaded or created files. This view is essential for navigating atoms, bonds, and molecules within larger projects.
You can open, edit, and switch between multiple documents for different workflows. Each document serves as a container, ensuring your data, structures, and any embedded files are well-organized and self-contained.
Embedding Related Files
One of SAMSON’s standout features is its ability to embed files and folders into documents. From Python scripts and computational models to research papers and data, you can make your document self-contained by using the following options:
- Drag and drop files into SAMSON — you’ll be prompted to embed them.
- Navigate to Home > Embed files or Home > Embed folders to embed content.
Embedded content remains part of your document, making it easy to transfer data between collaborators or machines without worrying about external dependencies. Learn more about sharing these enhanced documents here.
Final Thoughts
Loading molecules and associated resources in SAMSON is designed to be intuitive and versatile. From local files to online structures and fully embedded projects, SAMSON equips you with the tools to start your modeling work efficiently. To dive deeper into SAMSON’s capabilities, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today at SAMSON Connect.