One of the most crucial steps in molecular modeling is effectively loading your molecular structures into the software you are using. As a molecular modeler, this task might involve significant pain points: missing formats, confusing workflows, or cumbersome processes when switching between files and documents. In this blog post, we’ll look at how SAMSON, the integrative molecular design platform, makes loading molecules a straightforward and efficient process.
Why Loading Molecules Matters
Loading molecular data efficiently is vital. It lets you transition to the actual analysis, simulations, or editing with minimal waiting time. If you’re switching between formats, uploading composite documents, or embedding additional data for a holistic project, each step must feel intuitive. That’s the experience SAMSON aims to deliver.
Opening Local Files and Fetching Structures
SAMSON supports a wide variety of molecular formats, making it easier for users to integrate diverse datasets. To open a molecule structure from your local files:
- Use the top menu navigation: Home > File > Open.
- If shortcuts are more your style, press
Ctrl+Oon Windows/Linux orCmd+Oon macOS (think “O” for Open).
The platform also caters to those frequently switching between files. You’ll find recently opened files neatly listed under Home > File > Recent, with one-click access to revisit past work.
For advanced users, SAMSON employs a variety of file importers to recognize and import molecular formats automatically. Popular formats such as PDB, mmCIF/PDBx, and MMTF are supported by default, and additional importers for niche needs can be found on the SAMSON Connect Marketplace.
First-time import processes are exceptionally user-friendly, as importer settings are auto-configured but customizable. Adjust these preferences as needed, and SAMSON will remember them for your next session. Once ready, click OK or press Enter, and your molecule is loaded!
Working With Online Structures
If your molecular data is stored remotely, SAMSON won’t leave you stranded. You can use dedicated apps such as Fetch Structures, accessible under Home > Fetch. This feature downloads molecular structures directly from sources like the RCSB Protein Data Bank. It’s a seamless option when working with public data.
Maximizing Document Management
Once you’ve loaded molecules, SAMSON places them in an active document. The Document view interface then displays all embedded data, including molecules, atoms, bonds, and even non-molecular content like images and Python apps. A handy feature is that you can have multiple documents open simultaneously and switch between them via Home > Documents. Need more efficiency navigating documents? Use shortcuts like Ctrl+Tab (Windows/Linux) or Cmd+Tab (Mac).
Embedding and Sharing Made Simple
Beyond loading molecules, SAMSON also supports embedding entire files and folders within documents. Drag and drop files—whether Python scripts, images, or research papers—directly into SAMSON. Embedded materials make your project fully portable, meaning you can share it with collaborators seamlessly, or transfer it to another system without missing content.
Ready to Go Further?
Efficient molecular loading is the first step toward deep scientific exploration—be it inspecting, editing, simulating, or sharing structures. That’s why SAMSON puts a well-thought-out, user-friendly process at your fingertips.
For a more detailed guide, visit the official SAMSON documentation here: https://documentation.samson-connect.net/users/latest/loading-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. Start using SAMSON today by downloading it from SAMSON Connect.