SAMSON supports a number of formats for importing and exporting various data (molecular systems, meshes, etc).
SAMSON can also embed almost any type of file (scripts, PDFs, images, data, etc.) into SAMSON Documents.
Thanks to the Code Editor in SAMSON you can also open, edit, and save any text (non-binary) file, including Python scripts.
Below is a non-comprehensive list of formats supported in SAMSON for importing and exporting various types of data. Most of these formats are available with SAMSON right away, but for some, it is necessary to add an extension (click on the extension link). Please note that SAMSON Extensions might support additional formats that are not listed here.
SAMSON formats
SAMSON has its own formats (SAM, SAMX) that support an extensive variety of types of data that can be opened, created, and saved by SAMSON, among them are molecular structures (Structural models, etc.), groups, Vms,, meshes, animations, notes, simulators (interaction models and state updaters), etc. SAMSON formats can also embed folders and files (scripts, PDFs, images, data, etc.).
| File type | Description | Read | Write |
|---|---|---|---|
| SAM | SAMSON binary format | ✓ | ✓ |
| SAMX | SAMSON XML format | ✓ | ✓ |
Molecular structures
| File type | Description | Read | Write |
|---|---|---|---|
| ARC | Tinker format | ✓ | ✓ |
| CIF | Crystallographic Information File - CIF for crystal structures via Crystal Creator App - The macromolecular Crystallographic Information File (mmCIF). Aliases: PDBx, mmCIF | ✓ | ✓ (PDBx/mmCIF format) |
| CML | Chemical Markup Language file | ✓ | ✓ |
| CSSR | SERC Daresbury Laboratory's Cambridge Structure Search and Retrieval (CSSR) file | ✓ | ✓ |
| GRO | GROMACS structure file | ✓ | ✓ |
| GZ | GZ archive file | ✓ | |
| LMP, LMPDATA | LAMMPS Data file. Alias for read: DATA | ✓ | ✓ |
| MMTF | The Macromolecular Transmission Format (MMTF) file | ✓ | |
| MOL2 | Tripos MOL2 file | ✓ | ✓ |
| MOLDEN | Molden file | ✓ | |
| PDB | Standard PDB file. Aliases for read: ENT, VDB, PDB1, PDB2, etc. | ✓ | ✓ |
| PDBQT | PDBQT file | *ADVE | *ADVE |
| PSF | CHARMM, NAMD protein structure file (PSF) file | ✓ | |
| PARM7, PRMTOP | AMBER topology file, used when loading AMBER NetCDF trajectories | ✓ | |
| SDF | Chemical table file (CT File) format. Supports V2000 and V3000. Aliases for read: MOL, SD | ✓ | ✓ |
| SMI | SMILES file | *SM | ✓ |
| TOP | GROMACS topology file | ✓ | *GW |
| TPR | GROMACS run topology file | ✓ | *GW |
| XYZ | A simple coordinate trajectory format | ✓ | ✓ |
ADVE - PDBQT files can be generated with AutoDock Vina Extended extension which can also load PDBQT files from docking projects done using AutoDock Vina Extended.
SM - SMILES can be read and generated with SMILES Manager extension.
GW - GROMACS project files can be generated with GROMACS Wizard extension.
Molecular trajectories
| File type | Description | Read | Write |
|---|---|---|---|
| ARC | Tinker format | ✓ | |
| DCD | CHARMM, NAMD, or LAMMPS binary trajectory | ✓ | ✓ |
| LAMMPSTRJ | LAMMPS ASCII trajectory written by the LAMMPS dump command | ✓ | |
| NC | AMBER NetCDF format. Aliases for read: NCDF, NCTRAJ | ✓ | ✓ |
| PDB | Standard PDB file. Aliases for read: ENT, VDB, PDB1, PDB2, etc. | ✓ | ✓ |
| TNG | Trajectory Next Generation file | ✓ | |
| TRR | GROMACS TRR trajectory | ✓ | ✓ |
| TRJ | GROMACS TRJ trajectory format | ✓ | |
| XTC | GROMACS compressed trajectory | ✓ | ✓ |
| XYZ | A simple coordinate trajectory format | ✓ |
To read and write some of the trajectory formats, SAMSON uses the chemfiles library.
3D geometries
SAMSON loads 3D geometries as meshes.
SAMSON can export the following nodes as 3D geometries: Structural models, Visual models (if such functionality is implemented for this visual model), and meshes.
| File type | Description | Read | Write |
|---|---|---|---|
| OBJ | Wavefront OBJ file | ✓ | ✓ |
| glTF | GL Transmission Format | ✓ | ✓ |
| STL | ✓ |
Python scripts
Please refer to the Scripting page to learn how to use Python scripts in SAMSON.
| File type | Description | Read | Write |
|---|---|---|---|
| PY | Python scripts | ✓ | ✓ |
Images
Images are loaded as meshes.
To save an image, use Capture.
| File type | Read | Write |
|---|---|---|
| BMP | ✓ | ✓ |
| JPG | ✓ | ✓ |
| PNG | ✓ | ✓ |
| GIF | ✓ | |
| PBM | ✓ | |
| PPM | ✓ | |
| XBM | ✓ | |
| XPM | ✓ |
GIF is loaded not as an animation but only as a single image.
Movies or animations
Animations in SAMSON can be saved as movies. Please refer to the Presenting and animating page to learn how to create and save animations in SAMSON.
| File type | Read | Write |
|---|---|---|
| GIF | ✓ | |
| MP4 | ✓ | |
| WEBM | ✓ |
DNA origami
The formats for DNA origami are supported by the Adenita extension.
| File type | Description | Read | Write |
|---|---|---|---|
| ADN | Adenita format | ✓ | ✓ |
| ADNPART | Adenita parts format | ✓ | ✓ |
| JSON | Cadnano or legacy Adenita parts format | ✓ | ✓ |
| PLY | Cadnano mesh | ✓ | ✓ |
Adding a new format
If SAMSON does not support a file format that you would like to use and you would like us to add it to SAMSON, then please contact us via the SAMSON Connect Forum.
You can also develop your own importers and exporters. Please refer to the documentation about generating SAMSON Extensions and the Documentation center for more information about writing new importers for SAMSON.