A molecular modeling workflow rarely stays inside one tool. You may need to import a structure, prepare or edit it, run a calculation, inspect the results, and export data for another application. The frustrating part is often not any single step—it is the gaps between them: a missing file reader, a visualization you need, or a specialized method that is not part of your current setup.
SAMSON addresses these gaps through extensions: modules that add capabilities to the platform. Rather than treating every new need as a reason to change your whole workflow, you can look for an extension that supplies the particular function you are missing.
Start with the missing step
Before searching for a tool, describe the task you cannot complete. The kind of work you need to do is a useful guide to the kind of extension to look for:
- Need to open or save a particular file format? Look for an importer or exporter. Importers parse files, while exporters write document content to files. Examples include PDB and XYZ tools.
- Need to interact with or modify a structure? An editor may provide a focused operation, such as selecting a region, applying a rigid-body transform, deforming a model while preserving local rigidity, or generating a nanotube.
- Need a different way to inspect data? Visual models provide representations in the viewport. Examples include protein secondary structure, electron-density isosurfaces, and volume rendering of an electrostatics field.
- Need to calculate energies and forces or advance a simulation? Interaction models handle energies and forces; state updaters implement methods for advancing simulation states. Examples include elastic network models, minimization, Monte Carlo, and molecular dynamics methods.
- Need a broader workflow or connection? Apps can provide new functionality, connect to an external executable or web service, or integrate existing code with SAMSON and other extensions.
This distinction helps narrow the search. For example, if a structure is already in the document but you need a new way to manipulate it, an editor is a more relevant starting point than an importer. If the issue is how results appear, look at visual models rather than simulation methods.
Find and add what you need
Extensions are available through SAMSON Connect. Sign in to your account, open the SAMSON Connect Marketplace, and choose the extensions relevant to your work. SAMSON downloads a default set of extensions the first time it starts; additional ones can be added later, so you do not need to decide on every capability at the outset.
Once an app is available, you can start it from Home > Apps or search for it with the Find everything box. Editors are accessed from the left-side menu of the viewport. Other extension types contribute capabilities such as file parsing, export, visual representation, or simulation methods.
A useful way to evaluate a candidate extension is to ask three questions: Does it address a specific step in my workflow? Does it work with the kind of content or method I need? And do I need an interactive tool, a visualization, file support, or a calculation? These questions keep the search grounded in the modeling task rather than in a long list of features.
When the tool you need does not exist
If an available extension does not cover your use case, SAMSON can also be extended through development. The SAMSON SDK is available from the Download page after signing in to SAMSON Connect. It supports creating apps, editors, force fields, services, and other extensions, with code templates intended to help developers get started. Existing code can also be integrated into SAMSON rather than rebuilt from scratch.
Not every automation need requires a compiled extension: SAMSON’s scripting documentation describes another route for automating workflows. For developers who do build an extension, it can be distributed through SAMSON Connect as a free offering or through subscriptions, including different monthly or yearly tiers.
The practical takeaway is simple: identify the point where your molecular workflow gets stuck, then look for the extension category that matches that task. Add a focused capability when it exists; consider scripting or SDK development when you need a custom solution. For details on extension types, adding them, and developing or distributing your own, learn more in the SAMSON documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.