For molecular modelers, one of the biggest challenges is ensuring interoperability between tools and formats. When working with diverse datasets, simulations, or visualizations, ensuring that your software supports the correct file formats can save countless hours of frustration. Fortunately, the SAMSON molecular design platform supports a plethora of formats for importing, exporting, and managing data efficiently.
SAMSON’s Own File Formats
SAMSON supports its proprietary file formats, SAM and SAMX. These formats allow the import, export, and storage of diverse data types, including molecular structures, meshes, animations, notes, and simulators. What sets SAM and SAMX apart is their ability to embed folders and files, such as scripts, PDFs, and images, directly within SAMSON Documents. This is particularly useful when organizing and sharing projects with collaborators.
Here’s the functionality at a glance:
- SAM: A binary format for robust data storage.
- SAMX: An XML-based format providing better readability and exchangeability.
Handling Molecular Structures
SAMSON supports a wide variety of molecular structure file formats, making it a truly flexible tool. Whether you’re working with small molecules, macromolecular structures, or simulations, there’s likely support:
- ARC: Used in Tinker tools.
- CIF: Crystallographic data files, including support for mmCIF.
- GRO, TOP, TRR: Compatible with GROMACS topologies and trajectories.
- MMTF: A lightweight macromolecular format.
- PDB: The widely used standard for macromolecular structures.
Extensions augment SAMSON’s capabilities further. For example, the Crystal Creator app adds specific functionality for handling CIF files. Additionally, there’s built-in support for chemical formats like SMILES and SDF, with extensions offering SMILES management features.
Molecular Trajectories
Analyzing trajectory formats for simulations becomes seamless with SAMSON’s range of supported formats. From GROMACS TRR to AMBER’s NetCDF, SAMSON leverages the chemfiles library for advanced trajectory handling. Importantly, these formats include:
- NC (NetCDF): Widely used for AMBER simulations.
- TRR: The GROMACS trajectory format.
- PDB: Extending the traditional PDB usage to trajectories.
3D Geometries and Visualization
For creating high-quality visualizations and simulations, SAMSON can load and export 3D geometries. Supported formats include:
- OBJ: A standard format for 3D modeling.
- glTF: Optimized for 3D transmission and graphics rendering.
- STL: Widely used for 3D printing and design.
This capability allows users to not only create stunning molecular animations but also integrate seamlessly within broader design workflows.
Easy Script Integration
For those incorporating custom scripts into their workflows, SAMSON supports Python directly. Python (.py files) can be read, edited, and executed using SAMSON’s built-in Code Editor. This makes it feasible to customize molecular design workflows without leaving the platform.
Additional Support for Images and Movies
To further enhance molecular modeling presentations, SAMSON supports importing images in various formats (e.g., BMP, JPG, PNG) as meshes and allows exporting animations as videos in GIF, MP4, and WebM formats. This is particularly useful for sharing molecular dynamics results or creating educational content.
DNA Origami with Adenita
For researchers designing DNA origami structures, SAMSON integrates with the Adenita extension, supporting formats like ADN, ADNPART, and JSON. Whether working with Cadnano or designing parts for a project, the extensibility offers comprehensive support for nanotechnology structures.
Customize with Extensions
If your needed file format isn’t supported out of the box, SAMSON allows users to develop custom importers and exporters. By following the Extension Generator guide, you can build the tools you need for your specific projects.
For a detailed list of all supported formats and further information, visit the SAMSON Supported Formats documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at this link.