If you’ve ever spent time converting molecular systems between different file formats just to open them in various tools, you’re not alone. For molecular modelers working with crystallography data, MD simulations, mesh geometries, or even animations, incompatible formats can be a constant source of friction.
SAMSON, the integrative platform for molecular design, might lighten your load more than you expected. One of the lesser-known strengths of SAMSON is its wide — and indeed, surprising — support for a broad spectrum of file formats. From crystal data to molecular dynamics trajectories, SAMSON acts as a hub where most of your molecular data can be imported, exported, viewed, edited, and even scripted in Python.
Why it matters
There’s no shortage of file types in molecular modeling:
- PDB, CIF, MOL2 for molecules
- DCD, TRR, XTC for molecular dynamics trajectories
- OBJ, STL, glTF for 3D meshes and geometries
- PY for Python scripting inside SAMSON
- MP4, WEBM for animations
- SAM, SAMX for SAMSON-native document formats
Usually, using separate tools for each of these means frequent file-type juggling. Here, SAMSON could centralize your workflow.
What you can do in SAMSON
- Open and save PDB, mmCIF, MOL2, SDF, and many more molecular structure files. SAMSON can even deal with GROMACS and AMBER files through extensions.
- Load entire simulations via formats like DCD, TRR, XTC, LAMMPSTRJ. Want to replay frames or export snapshots? SAMSON can do that too.
- Create publication visuals or export geometry data in OBJ, STL, glTF formats for post-processing or 3D printing.
- Capture animations and playable videos in MP4, WEBM, or GIF.
- Embed scripts, datasets, or citations using the SAM or SAMX formats, which can include folders and external files.
Notably, you can use the Code Editor within SAMSON to directly edit and run Python scripts. Any readable text file, including configurations and datasets, can be handled outright in the platform — no need to juggle external editors.
DNA origami and more
If you’re working in DNA nanotechnology, SAMSON also supports specialized formats like ADN, ADNPART, and JSON (Cadnano), with help from the Adenita extension.
Where to look?
Here’s the best part: the full format support is documented clearly. If a format isn’t supported natively, SAMSON Extensions can usually bridge the gap. And if needed, users can even write their own importers/exporters.
You can explore the complete list of supported formats, including whether each format supports reading, writing, or both, in the official documentation:
For molecular modelers wanting to reduce complexity and streamline their work, being able to access and interact with such a wide variety of formats directly in one platform can be a game changer.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.