Molecular designers often face challenges when working with diverse data formats. What formats will their tools support? Are additional extensions required? If you’re using SAMSON, the integrative molecular design platform, understanding supported data formats can significantly streamline your workflow. Here’s a guide to SAMSON’s built-in compatibility and its extensive capabilities for working with an array of formats.
SAMSON’s Native Formats: SAM and SAMX
SAMSON has its proprietary formats—SAM (binary) and SAMX (XML). These formats are highly versatile, allowing users to embed all kinds of data, such as molecular structures, animations, scripts, PDFs, simulators, and more, directly into SAMSON Documents. This simplifies data management by consolidating different file types into a single container, enabling seamless sharing and reuse within projects.
Broad Support for Molecular Structures
SAMSON is built to support a wide range of file types for molecular structures. Here are some examples:
- Standard PDB (Protein Data Bank) Files: Read and write standard structural files used by macromolecular researchers.
- CIF and mmCIF: These crystallographic data formats are commonly used in computational chemistry and structural biology. Easily integrate them into your projects using the Crystal Creator App.
- SMI (SMILES): Read and generate SMILES strings with SAMSON’s core functionality or by using the additional SMILES Manager extension.
- SDF: Chemical table files (CT Files) supporting both V2000 and V3000 variants allow easy handling of chemical databases.
Molecular Trajectories and Geometries
For molecular simulations and structural analyses, SAMSON shines when it comes to trajectory data:
- Common Trajectory Formats Supported: These include DCD, TRR, XTC, and Amber’s NetCDF trajectories. You can easily read and write them for further analysis.
- Coordinate Formats: XYZ and ARC formats are accessible for reading and writing simple coordinate files or simulation snapshots.
In 3D design and visualization, SAMSON supports 3D mesh formats such as OBJ, glTF, and STL. This makes it easy to convert molecular structures into geometries for external processing or visualization.
Extending Capabilities with SAMSON Extensions
Out of the box, SAMSON supports numerous formats, yet its modular design allows you to expand its functionality. Many SAMSON Extensions offer additional file compatibility. For example:
- AutoDock Vina Extended: This extension facilitates reading and generating PDBQT files used in docking projects.
- Adenita: For DNA origami enthusiasts, the Adenita extension supports specialized formats like ADN or JSON.
- GROMACS Wizard: This extension allows intuitive preparation of GROMACS project files (e.g., TOP, TPR).
SAMSON Extensions are easy to install and empower you to tailor the platform to match your unique workflow requirements.
Beyond What Is Supported: Adding Formats
If SAMSON does not support a file format you frequently use, you’re not out of options. You can request new support via the SAMSON Connect Forum. Alternatively, advanced users can create their own importers and exporters by developing custom extensions. Check out more details in the Extension Generator documentation.
Conclusion
With its extensive format support, SAMSON is a highly flexible tool for any molecular modeler. Whether you’re working with macromolecular data, exploring geometries for 3D printing, or analyzing trajectory files, SAMSON delivers powerful capabilities right out of the box. For a complete overview of supported formats, visit the full Supported Formats documentation.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.