Sharing and storing molecular models outside the design environment is an essential part of a molecular modeler’s daily work. Whether you’re preparing data for a publication, collaborating with colleagues, or setting up simulations in another tool, exporting your models in the right format saves both time and headaches. SAMSON, the integrative molecular design platform, supports this need with a practical and extensible exporting system.
Why exporting matters 🧬
Working on complex biomolecular structures or simulations often involves switching between different software environments. Perhaps you’re visualizing results in SAMSON, then need to process them in GROMACS, or share them as a simplified structure with a collaborator who only uses PyMOL. Each use case may require a different file format.
Having quick access to reliable exporters is crucial to avoid frustration when trying to match your workflow or the requirements of external tools.
Built-in SAMSON Exporters
SAMSON comes with a set of built-in exporters that allow you to write your molecular structures, models, and visualizations to standard chemical file formats. Examples include:
- PDB (Protein Data Bank format)
- XYZ (used for trajectories and simple molecular geometries)
These exporters help ensure compatibility with a range of downstream tools, including molecular dynamics packages and visualization software.
Can’t find the format you need?
If SAMSON doesn’t currently support a format your workflow requires, don’t panic. SAMSON supports many formats by default, but you can also explore SAMSON Connect to find additional exporters developed by the community or SAMSON’s own team. Still missing something? You can reach out via email.
Better yet: if you or someone on your team can develop one, SAMSON provides tools to create your own exporter extensions—adding support for any custom or rare format your project may depend on.
Do-it-yourself: Build your own exporter
SAMSON’s developer documentation offers a guideline for writing custom exporter extensions. This is especially useful if you’re developing a new workflow, working with proprietary data, or targeting lesser-known formats. Getting started is manageable thanks to:
- The Extension Generator
- The Documentation Center with detailed examples and API references
While this may require some knowledge of C++, it gives you full flexibility over how your data is exported, down to the atom level.
Conclusion
Exporting files in the right format might seem like a minor detail, but for molecular modeling workflows it can be a key step. SAMSON supports standard formats out of the box and encourages extensibility through its Connect platform and custom development tools. This way, you can spend more time designing and analyzing, and less time wrestling with file conversions.
Learn more about SAMSON Exporters.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.