For molecular modelers, having a streamlined and reliable process for loading molecular structures is essential. Whether you are visualizing locally stored files, fetching complex structures from online databases, or embedding project materials, seamless integration is vital for workflows. In this post, we will introduce the basics of loading molecules in SAMSON, an integrative molecular design platform, and highlight key features to get you started.
Opening Local Files and Fetching Structures
Loading molecules in SAMSON is straightforward, whether your data resides on your local system or in external databases. To open a molecule from a file, navigate to Home > File > Open or use the appropriate keyboard shortcut:
Ctrl + O(on Windows/Linux)Cmd + O(on Mac)
If you need to revisit recent files, go to Home > File > Recent, where a list of previously opened files is readily accessible.
The robust importing system in SAMSON automatically identifies the right file format and uses the correct importer. Supported formats include PDB, mmCIF, MMTF, and more. For users needing additional file format support, exploring new importers via the Marketplace on SAMSON Connect is highly recommended.
Setting Importer Parameters
SAMSON’s importers are designed with customizable parameters to handle varied file formats and specific scientific needs. Parameters are set to default during the first use, ensuring the process is uncomplicated. If adjustments are necessary, these settings can be modified and saved for future imports. The following image shows a typical importer dialog box for PDB files:
After confirming your settings, press OK or simply hit Enter, and enjoy a smooth import experience. Your molecular structure will then appear in the Document view and the viewport, ready for visualization, simulation, or editing!
Fetching Structures from Online Databases
SAMSON’s integrated Fetch Structures functionality empowers researchers to directly download molecular structures from resources like the RCSB Protein Data Bank. To do so, simply navigate to Home > Fetch, where you can fetch PDB, mmCIF, or MMTF format files. This eliminates the need for manual downloads and accelerates the process of loading biologically relevant models into your workspace.
Pro Tip: Embedding Files and Folders
Did you know that SAMSON allows you to embed additional resources within your documents? Whether it’s Python scripts, datasets, or entire folders, SAMSON’s Universal File Embedding ensures that everything stays self-contained. Use drag-and-drop functionality or access Home > Embed files and Home > Embed folders. Embedded files help you maintain an organized workflow and simplify file sharing.
Next Steps
Once you’ve successfully loaded your molecules, there are several exciting directions to explore:
- To inspect, measure, or analyze your structure, proceed to Work with Structures.
- Planning to edit or design new systems? Check out Building Molecules.
- For sharing your finished work, visit Share Documents.
Leveraging SAMSON’s molecule loading capabilities can significantly improve your molecular modeling workflows. For more detailed information, visit the official documentation: Loading molecules.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at SAMSON Connect.