Molecular modelers often face challenges when it comes to efficiently loading molecular structures into their tools. Whether you’re working with local files, fetching data from external databases, or dealing with multiple document setups, clarity and flexibility are key. This is where SAMSON’s integrative platform provides a solution, designed to make the process intuitive and efficient.
The Basics of Loading Molecules in SAMSON
When you’re ready to dive into molecular modeling within SAMSON, one of the first steps is bringing your content into the platform. You can start by either opening local files or fetching molecular structures from external databases, making it versatile for various workflows.
Loading Local Files
The process of loading molecules in SAMSON is straightforward. To open local files, navigate to:
- Home > File > Open, or
- Use the keyboard shortcut
Ctrl + Oon Windows/Linux, orCmd + Oon Mac.
If you wish to reopen a recently accessed file, SAMSON provides a recent file list under Home > File > Recent.
SAMSON automatically selects the appropriate importer based on the file format of the structure you are loading. These importers can handle numerous standard file formats used in molecular modeling. If you need support for additional formats, you can browse the SAMSON Connect Marketplace for other importers.
Depending on the importer and file format, you may need to configure specific parameters during the import process. These parameters are customizable and are saved for future use once modified, making your workflows more efficient over time. After setting the parameters, press OK or hit the Enter key to load your structure. The molecule will then appear in both the Document view and the viewport.
Fetching Structures
If your workflow involves obtaining molecular structures from external sources, SAMSON’s Fetch Structures app provides seamless access to data from resources like the RCSB Protein Data Bank. You can download files in PDB, mmCIF/PDBx, or MMTF formats directly into your document, allowing for a quick transition to analysis or modeling tasks.
Managing and Switching Documents
SAMSON’s document system is another core feature that simplifies molecular modeling. Documents store all relevant information about atoms, bonds, molecules, and more in an organized way. While working, you can maintain multiple documents simultaneously and switch between them as needed. This is particularly helpful when you are handling complex projects or copying structures between different documents.
The Document view gives an overview of the data graph for the active document, ensuring that all your loaded structures and related information are easy to locate and manage.
Creating a new document or switching between existing ones is just as intuitive. Follow Home > File > New to start fresh or use Home > Documents to navigate between opened documents easily.
Why SAMSON is a Game-Changer
The flexibility and user-friendly design of SAMSON’s molecule loading process, combined with its document management features, make it easier for molecular modelers to focus on science instead of software. Whether you need to load local files, fetch new structures, or organize complex projects, SAMSON streamlines your workflows effectively.
To learn more about how to load molecules and manage documents in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON from SAMSON Connect.