Importing molecular structure files is often the first step in every modeling project. Whether you’re working with proteins, small molecules, or large assemblies, you likely start by loading existing data from databases or experimental results. However, many researchers face a recurring obstacle: their file won’t open in their design platform—often because the format isn’t supported out of the box.
If you’re using SAMSON, this issue might be easier to address than you think. This blog post explores how SAMSON handles molecular file import, what to do when it doesn’t work, and how to extend its capabilities for specialized needs.
Why some files can’t be opened
SAMSON supports a broad set of molecular file types, including widely used formats like PDB, MOL2, and CIF. But with over 50 chemical formats in use across research domains, it’s not possible for any platform to support all of them by default.
This can be frustrating if:
- You received raw data from an experiment (e.g., electron density maps or cryo-EM reconstructions).
- The file format is specific to a domain or tool (e.g., a proprietary modeling format).
- The file itself is valid, but SAMSON doesn’t recognize it because an appropriate parser is not installed.
Using importers in SAMSON
In SAMSON, importers are extensions that parse different file formats into objects you can work with. Several essential importers come pre-installed, but many more are available through SAMSON Connect — a hub from which you can add new capabilities in just a few clicks.
If you ever encounter a file that SAMSON doesn’t open, the first thing to check is whether there’s an importer you can install from SAMSON Connect to enable support for that format. For example, if you’re working with volumetric data or specific simulation outputs, there might be specialized importers ready to parse that data.
See the full list of formats supported by SAMSON.
Custom importers: What if the format isn’t supported yet?
If you can’t find the right importer, there’s still hope. SAMSON allows you to create your own importers by developing a SAMSON Extension. Using the Extension Generator, you can start building an importer tailored to your needs.
This is especially useful in research groups developing custom simulation methods or working with proprietary output files. By writing your own parser, you make SAMSON compatible with your own data workflows.
And if you believe a format should be officially supported, you can always contact the SAMSON team to request it.
Use cases from the community
Here are a few common reasons users have turned to importers:
- Protein structure modeling: Bringing in electron density maps alongside PDB structures.
- Simulation post-processing: Importing trajectory outputs using custom formats.
- Academic sharing: Converting lab-specific formats into shareable models for collaboration.
If you’re a developer or want to automate part of your workflow, learning how to write an importer could save you time in the long run.
To learn more about file import in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/users/latest/importers/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.