One of the most common pain points for molecular modelers is getting their data—atomic and structural information, visualizations, and simulation results—out of their modeling platform in a usable format. Whether you’re sharing your research, preparing input for a simulation engine, or backing up your results, exporting your models correctly is crucial. Fortunately, SAMSON, the integrative platform for molecular design, provides flexible tools for exporting files in various formats.
Meet the Exporters in SAMSON
In SAMSON, Exporters are dedicated tools that allow you to save your document contents to external files. This can include atomic structures, simulation frames, and molecular visualizations. Examples include the PDB Exporter, XYZ Exporter, and other format-specific tools.
This built-in functionality helps researchers maintain compatibility with widely-used molecular simulation tools such as GROMACS, LAMMPS, or visualization packages. The export feature is particularly helpful when preparing files for collaboration, generating publication-ready data, or processing structures in downstream applications.
Why Exporting Can Be Tricky
Most molecular formats are very specific regarding what they store and how they store it. For example, the PDB (Protein Data Bank) format has strict formatting rules and is limited in the type and number of atoms it can represent. On the other hand, the XYZ format is quite flexible but lacks connectivity data like bonds or residues.
This means modelers need to choose the export format carefully, according to the aim:
- Are you feeding the output into a simulation engine?
- Do you want to keep detailed molecular annotations?
- Are you exporting snapshots from a trajectory or static structures?
Understanding your use case helps in choosing the right format.
How SAMSON Helps
SAMSON provides a series of exporters that can handle all of the above and more. These come pre-installed and ready to use. To use them:
- Select the model or structure you want to export in the SAMSON workspace.
- Choose the appropriate exporter from the Export menu.
- Specify the file format (e.g., .pdb, .xyz) and destination.
If you find that the format you need is missing, you can check the list of supported export formats. If it is not available, you’re invited to contact the SAMSON team.
Custom Exporting: How Far Can You Go?
Advanced users and developers can go further by building their own custom exporters through SAMSON Extensions. If you know how to code and want to tailor the export formats to match your specific pipeline, you can refer to the resources for developers:
This adds significant value for teams with specialized needs or proprietary file formats.
Tip: You can manage and install additional exporters via SAMSON Connect, the extension hub that allows you to plug in more capabilities.
If you regularly work with complex data pipelines, having exporting configured correctly can save hours when scaling or automating your workflows.
To explore more about exporters in SAMSON, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.
