When working with molecular models in SAMSON, it’s common to reach a point where you need to share your work with collaborators, include it in reports, or run external simulations. For many researchers, one of the first challenges is figuring out how to export structures and visual representations into formats others can use.
Let’s face it: with so many file types in computational chemistry—PDB, XYZ, MOL2, and more—it can be a bit overwhelming. The good news? SAMSON simplifies this process through its Exporter system.
What are Exporters in SAMSON?
In SAMSON, Exporters are tools designed to save content from your document—whether it’s the molecular structure or a visual scene—into a file. These exporters allow you to convert your SAMSON project into various standard file formats used in molecular modeling. Some exporters are available by default, while others can be installed on demand from SAMSON Connect.
Common Use Cases for Exporting
- Sharing with collaborators who use other tools like PyMOL, Chimera, or VMD.
- Running external simulations in software such as GROMACS, AMBER, or Gaussian.
- Preparing input files for docking studies, MD simulations, or quantum calculations.
- Capturing visualizations for research papers, posters, or presentations.
How to Export in Practice
Using an exporter in SAMSON is straightforward. After preparing your document:
- Open the File menu or right-click your structure.
- Choose the desired export format (e.g., PDB, XYZ).
- Configure any required export settings.
- Save the file to your preferred location.
The choice of exporter depends on what the recipient needs or the requirements of downstream software. For instance, if you’re sharing with a colleague who uses PyMOL, a PDB file is usually best. For quantum calculations, an XYZ or MOL2 file might be more appropriate.
What If the Exporter You Need Is Missing?
If the format you need isn’t listed, you’re not out of luck. You can:
- Check the full list of supported formats.
- Install additional exporters from SAMSON Connect.
- Develop your own exporter using the SAMSON Extension Generator.
- Reach out to the SAMSON team directly at contact@samson-connect.net.
If you’re comfortable with coding, custom exporter development based on the Extension Generator can help you adapt SAMSON to very specific needs. For example, if you’re working with custom data or niche simulation engines, building an exporter tailored to your pipeline could save hours down the line.
Conclusion
Exporting content from SAMSON isn’t just a convenience—it’s key to integrating your work into broader research workflows. Whether you’re submitting a structure for publication, running simulations elsewhere, or simply backing up your work in a readable format, exporters help make your research more portable and reproducible.
To explore the exporters available in SAMSON and how to use them effectively, visit the full documentation at 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.