Anyone working in molecular modeling has faced this at least once: after spending hours crafting a molecular structure, either to simulate a reaction, visualize an experimental result, or design a new molecule, you suddenly need to export it—to quickly share with collaborators, prepare for simulation, or submit for analysis. But then comes the question: what’s the right format? Do I have the right tools? And why didn’t I bookmark that export guide?
Structure export may not be the most exciting part of molecular modeling, but it is critical for sharing your work, connecting with other software tools, or archiving progress. Let’s walk through how SAMSON, the integrative molecular design platform, simplifies this often-overlooked part of the workflow—and how you can take full advantage of the tools provided.
What are Exporters in SAMSON?
Exporters in SAMSON are dedicated modules that help you write molecular structures and visualization states to files. These may include formats like PDB for crystallography or structural biology, XYZ for atom positions, or other niche formats used in simulation tools or visualization packages.
By default, SAMSON provides multiple exporters out of the box. For example, if you’re modeling a protein and want to carry out a simulation in GROMACS, you might rely on SAMSON’s PDB exporter. Or, if you’re visualizing a custom molecule and need it in XYZ for analysis, that’s just a few clicks away.
Why Exporting Is More Than Just Saving a File
Exporting is often part of a chain of tools. Modeling in SAMSON might be just the first step in a pipeline that includes quantum calculations in ORCA, molecular dynamics in LAMMPS, or rendering in Blender. Choosing the right format early on prevents headaches down the line—from conversion mismatches to structural distortions.
What’s helpful in SAMSON is that exporters are structured to support data integrity. For example, PDB exporters ensure that atom naming conventions and chain identifiers are properly respected, which is essential if a third-party analysis platform expects strict adherence to these conventions.
And If the Format You Need Isn’t There?
Don’t worry—SAMSON Connect allows you to download more exporters directly from inside the platform. If a supported format isn’t available yet, the SAMSON team actively encourages suggestions. You can even contact them directly.
For developers or researchers with a scripting background, there is also a path to write custom exporters. The Extension Generator and the general Developer Documentation explain how you can create your own RAM-to-disk bridges for formats you rely on.
Supported Formats
SAMSON maintains a full list of supported formats, updated alongside the platform. Be sure to check this page before installing third-party exporters—your format may already be supported.
Summary
- SAMSON includes default exporters like PDB and XYZ to help you share and archive data.
- More exporters can be added via SAMSON Connect.
- If a format isn’t available, you can develop your own exporter or suggest one.
- Proper export enables seamless collaboration and integration with third-party tools.
To learn more and see the full list of exporters and supported formats, visit the official SAMSON documentation: https://documentation.samson-connect.net/users/latest/exporters/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.