When working on molecular modeling projects, exporting your results into the right file formats is a crucial step—whether you’re preparing datasets for collaborators, submitting to databases, or moving your models into other software tools. However, choosing the appropriate exporter, and ensuring your molecular data is correctly saved, can be more involved than it first appears.
Fortunately, SAMSON offers a built-in set of exporters that help translate molecular structures and visualizations into widely-used file formats like PDB, XYZ, and more. These exporters act as translators between the rich modeling environment in SAMSON and the external tools or academic workflows you might rely on.
What are SAMSON Exporters?
In simple terms, exporters are tools inside SAMSON designed to take your molecular document—including atoms, bonds, and visuals—and convert it into a file you can use elsewhere. Exporters might generate atomic coordinate files (like PDB or XYZ), 3D images for presentations, or even animated molecular trajectories depending on what you’ve built.
Why Choosing the Right Exporter Matters
Say you’ve spent hours building a simulation-ready protein-ligand complex or preparing a high-quality visualization for a grant report. Exporting it incorrectly can mean losing important structural data or ending up with a file that another tool can’t open or interpret. Each exporter supports a different data scope. For instance:
- The PDB exporter focuses on biological macromolecules and generally retains atomic information but may not support non-standard bonds or annotations.
- The XYZ exporter offers a minimalist representation—ideal for visualizing small molecules, but without residue or bond type information.
Understanding what each exporter keeps—and what it omits—is key to mastering molecular workflows.
Built-In vs. Community Exporters
SAMSON includes several exporters by default, offering compatibility with many tools used in research. But if your needs go beyond the basics, additional exporters are available via SAMSON Connect. Researchers and developers from around the world contribute extensions, including format-specific exporters for niche applications.
Still not seeing the format you need? SAMSON encourages users to get in touch or even build their own exporter extensions (more on that in a future post).
When Exported Files Don’t Look Right
“Why does my exported molecule appear incomplete or malformed in another program?” This is a common question—and often, the issue lies in how the exporter interpreted your structure. Double-check that the exporter you’ve chosen matches your target application’s requirements. Cross-validation is one of the best ways to prevent surprises when transitioning between tools.
Need a Full List of Supported Formats?
Before saving, it helps to review the full list of file formats supported by SAMSON. This ensures you pick the best structure for your research context.
To learn more about how to export molecular data from SAMSON, visit the official documentation page: https://documentation.samson-connect.net/users/latest/exporters/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.