Molecular modeling often requires loading, inspecting, and working with molecular structures from various formats. However, efficiently bringing external data into your modeling environment can sometimes become a frustrating hurdle. This guide delves into how SAMSON simplifies the process of loading molecular data, whether from local files or online resources, ensuring you can focus on your molecular design tasks rather than grappling with file compatibility or navigation challenges.
Loading Local Molecular Structures
To load a molecular file into SAMSON, users can navigate through the menu via Home > File > Open. Alternatively, keyboard shortcuts offer a faster option: use Ctrl+O on Windows/Linux or Cmd+O on Mac.
If you’ve worked on files recently, you can access them quickly via Home > File > Recent. This provides a convenient list of recently opened files, saving time by eliminating the need to search manually.
Smart Importer System
When a file is loaded, SAMSON automatically uses the appropriate importer based on the file format. By default, SAMSON supports a multitude of molecular formats (see the full list of supported formats). Import parameters can often be adjusted to better fit the specific needs of your project.
For example, when working with PDB files, the PDB importer dialog allows you to configure options before importing, such as chain handling or including hydrogen atoms. Each importer retains previously configured parameters, so you won’t need to reset them every time you use it.
Online Access to Molecular Structures
In addition to importing local files, SAMSON offers tools to fetch molecular structures from the web. For instance, with the Fetch Structures app (Home > Fetch), you can access molecular files directly from the RCSB Protein Data Bank in various formats such as PDB, mmCIF/PDBx, and MMTF. This significantly reduces the effort needed to find and load publicly available molecular data.
Working with Loaded Content
Once a file is successfully loaded, the molecular structure appears in the Document view and the main viewport. The document view serves as a central hub for interacting with the structure, allowing users to visually inspect the molecular data and prepare for workflows such as editing or simulation.
Having multiple documents open simultaneously is also possible, making it easier to copy structures or work on different molecules in parallel. To switch between documents, use the document dropdown menu at the top-left of the interface, or go via Home > Documents. Keeping track of multiple projects while maintaining organization has never been easier.
Next Steps
Loading molecular data is just the starting point of your journey. Depending on your goals, you can:
- Proceed to inspect or measure molecular properties in Work with structures.
- Head to Building molecules to construct or modify structures.
- Learn how to share projects with collaborators via the Share documents feature.
- Explore SAMSON’s collaborative tools by visiting Collaboration.
To dive deeper into this topic, please visit the official documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON at https://www.samson-connect.net.