For molecular modelers, dealing with a myriad of file formats can be a significant challenge. Whether it’s importing molecular structures, handling trajectories, or exporting data, each stage in the modeling workflow involves handling specific file types. The SAMSON platform addresses this pain by supporting an extensive range of file formats for different kinds of data. This blog post highlights some of the key supported formats in SAMSON and how they simplify molecular modeling workflows.
SAMSON-Specific File Formats
SAMSON utilizes two robust proprietary formats for handling complex data:
- SAM: A binary format for storing SAMSON data in a compact and efficient way.
- SAMX: An XML-based format that ensures extensibility for storing a variety of molecular and project-related information.
Both formats allow for storing complex structures such as molecular models, meshes, animations, simulators, and more. They even support embedding external files (e.g., scripts, PDFs, or images), making them highly versatile for integrative design projects.
Molecular Structures
Importing molecular structures is central to most workflows, and SAMSON supports a wide array of molecular formats. These include:
- PDB: The Protein Data Bank standard format, widely used for structural biology. SAMSON supports a variety of aliases for this format as well.
- CIF: The Crystallographic Information File, ideal for both crystal and macromolecular structure data.
- GRO: GROMACS structure files used in simulation workflows.
- MOL2 and SMILES: Commonly used in cheminformatics.
Extensions like the Crystal Creator and SMILES Manager further enhance compatibility, enabling molecular modelers to work with formats like CIF or generate SMILES notations directly within SAMSON.
Molecular Trajectories and 3D Geometries
SAMSON also shines when it comes to handling molecular trajectories and 3D geometries. Supported formats such as DCD (for CHARMM or NAMD), GROMACS trajectory formats (e.g., TRR or XTC), and XYZ ensure seamless integration of simulation outputs back into SAMSON for further analysis. For importing and exporting 3D geometries, SAMSON supports well-known formats like OBJ, glTF, and STL, which are often required for visualizations or printing.
Streamlined Image and Animation Handling
Molecular modelers often need to create high-quality visual representations of their work. SAMSON supports importing image files like BMP, JPG, and PNG, while also allowing animated presentations or movies to be exported in popular formats such as GIF, MP4, and WEBM. This capability provides modelers with everything they need to visually communicate their work effectively.
Extendability and Customization
In certain cases, SAMSON might not support a specific file format by default. However, the platform’s flexibility allows users to develop their own importers and exporters through SAMSON Extensions. Instructions for this are detailed in the SAMSON documentation, ensuring users can expand SAMSON’s functionality as needed.
To see the complete list of supported formats and learn how SAMSON manages them, visit the full documentation at SAMSON Supported Formats.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at SAMSON Connect.