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Supported formats

SAMSON supports a wide range of formats for importing and exporting various data (molecular systems, meshes, images, 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, visual models, 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, LMPDAT 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 Python Scripting page to learn how to use Python scripts in SAMSON.

File type Description Read Write Execute
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.