One of the common challenges for molecular modelers is dealing with the myriad of file formats across different software tools. Ensuring compatibility and smooth data exchange among platforms can often become a bottleneck in research workflows. If you are a user of SAMSON, the comprehensive molecular design platform, you’ll find that understanding its supported formats can be immensely useful in streamlining your projects.
The flexibility of SAMSON lies in its ability to support a wide range of file formats for importing and exporting molecular systems, meshes, images, and more. Furthermore, SAMSON doesn’t just stop at common formats—it even allows embedding almost any file type (e.g., scripts, images, and PDFs) into SAMSON Documents. This provides researchers with both a robust and consistent file handling workflow.
SAMSON-Specific Formats
At the heart of SAMSON are its own formats: SAM and SAMX. These formats are designed for extensive compatibility with molecular data. With SAMSON-specific formats, you can handle molecular structures (e.g., structural models), meshes, animations, and interaction models seamlessly. Another highlight is the ability of SAM and SAMX formats to embed scripts, PDFs, or any additional data directly into a document. This significantly simplifies projects that rely on diverse data sources.
Supported Formats for Molecular Structures
SAMSON supports many commonly used molecular file formats such as PDB, CIF, SDF, and SMILES, to name a few. For crystallographic studies, you’ll be pleased to know that CIF and its variations, including macromolecular CIF (mmCIF), are supported. Additionally, SAMSON accommodates other formats like XYZ (a simple coordinate trajectory format) and MOL2, ensuring a wide range of molecular modeling scenarios are covered.
Here’s an example table of some molecular formats supported for importing and exporting molecular structures:
| File Type | Description | Read | Write |
|---|---|---|---|
| PDB | Protein Data Bank format | ✔ | ✔ |
| XYZ | Simple coordinate trajectory format | ✔ | ✔ |
| SMI | SMILES file | ✔ | ✔ |
| SDF | Chemical Table File (supports V2000 and V3000 versions) | ✔ | ✔ |
For molecular trajectories, SAMSON facilitates file types like GROMACS TRR and XYZ formats. It uses libraries like Chemfiles to read and write some trajectory formats, offering increased flexibility for simulations.
3D Geometries and Images
If you work with 3D meshes or visual outputs, SAMSON supports formats such as OBJ, glTF, and STL for 3D geometries. Moreover, capturing images of your molecular systems is easy with formats such as PNG, JPG, and BMP supported for reading and writing.
Add New Formats
Have a format that’s not supported yet? SAMSON goes the extra mile to empower users by enabling them to develop their own importers and exporters. Developers can refer to SAMSON’s importers and exporters documentation to create customized solutions tailored to their unique needs.
For further details and a comprehensive list of supported formats, visit the official documentation page on Supported Formats.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON for free at https://www.samson-connect.net.