If you’re working in molecular modeling, you’re likely juggling various file formats—PDBs from protein databases, XYZs from quantum chemistry, CIFs from crystallography, and many more. Each software tends to have its own preferred formats, making compatibility an ongoing concern, especially when projects span multiple tools and collaborators.
SAMSON, the integrative platform for molecular design, tackles this challenge with support for dozens of file formats across molecular structures, trajectories, meshes, images, animations, and even scripts. The goal: allow you to focus on your science—not format conversions.
Molecular Structure Formats: A Quick Overview
SAMSON supports a broad array of molecular structure formats, both for reading and writing. This includes familiar names like:
- PDB: The standard Protein Data Bank format for macromolecules.
- SDF: Widely used for small molecules; both V2000 and V3000 versions are supported.
- CIF and mmCIF: Common in crystallographic databases, supported via the Crystal Creator App.
- SMILES (SMI): Read and write linear notations using the SMILES Manager Extension.
- MOL2: Great for molecular docking and force field data.
- GRO, LMP (LAMMPS), PSF, and TOP: Useful for simulation setups, especially integrated with tools like GROMACS, CHARMM, and NAMD.
SAMSON natively supports its own formats (SAM and SAMX), which allow you to embed not just the structure, but the entire modeling context—notes, scripts, hierarchy, and visual representations—into a single file.
Trajectory Formats: Keeping the Time Dimension
Dynamic molecular simulations produce large trajectory files. SAMSON lets you read and, in many cases, write formats like:
- DCD: Binary trajectories from CHARMM, NAMD, and LAMMPS.
- XTC/TRR/TRJ: GROMACS-friendly trajectory formats, both compressed and full data.
- NC (NetCDF): Used in AMBER simulations, with aliases like NCDF and NCTRAJ.
This means you can visualize and analyze simulations from different engines directly inside SAMSON—no need for format conversion tools in between.
Visualization and Export Options
If you need to communicate your findings visually, SAMSON supports exporting various models and visualizations to 3D geometry formats:
- OBJ: Wavefront geometry export.
- glTF: Ideal for web and real-time 3D applications.
These can be used in external renderers, CAD tools, or for presentations.
How SAMSON Handles Images and Scripts
SAMSON also lets you open and save images in multiple formats (JPG, PNG, BMP, GIF, etc.) and even execute and edit Python (.py) scripts directly inside the platform—useful for automating tasks, building extensions, or running custom calculations.
One Less Thing to Worry About
If you’ve ever interrupted your research to dig up a converter or debug formatting quirks between tools, SAMSON’s format support might ease that burden. Whether you’re importing from Pymol, exporting to AutoDock, simulating with GROMACS, or presenting through meshes and movies, it’s likely SAMSON can handle it.
To explore the complete (and frequently updated) list of supported formats in SAMSON—including specialized ones for DNA origami projects—visit the official documentation: https://documentation.samson-connect.net/users/latest/supported-formats/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.