A molecular modeling workflow rarely stays confined to one task. You may need to import a structure, inspect it in a particular way, modify it, run a calculation, and export the result. When the tools for those steps do not quite fit together, the temptation is to switch applications or build a workaround. In SAMSON, there is another option: add an extension that supplies the capability your workflow is missing.
The useful idea is that an extension is not necessarily a single, large application. SAMSON Extensions can provide focused pieces of functionality: apps, editors, importers, exporters, visual models, interaction models, and state updaters, among other elements. Thinking in terms of the task you need to accomplish makes it easier to identify what kind of extension to look for.
Start with the point of friction
Before searching for an extension, describe the problem as a concrete step in your work. For example: “I need to read this file format,” “I want to create a particular structure more quickly,” or “I need a different way to visualize a result.” This simple framing helps distinguish between extension types:
- Need to open or save a file? Look for an importer or exporter. Importers parse files; exporters write document content to files. The documentation gives PDB and XYZ as examples.
- Need a new way to interact with a document? An editor may provide a tool for a task such as selecting, transforming, or deforming structures. Editors are available from the left-side menu of the viewport.
- Need a specific representation? A visual model can change how information appears in the viewport, for example through a protein secondary-structure representation or an electron-density isosurface.
- Need calculation or simulation behavior? Interaction models compute energies and forces, while state updaters advance simulation states. The documentation lists examples such as elastic network models, minimization algorithms, and molecular dynamics algorithms.
- Need a broader workflow or connection? Apps can provide varied functionality, including connecting SAMSON to an external executable or web service, or integrating existing code.
These categories are a guide, not a requirement to understand the platform’s architecture before getting started. A useful first step is to search for an extension that matches the task. SAMSON includes a set of extensions by default when it is first started. To add or remove others, sign in to SAMSON Connect and choose them from the Marketplace.
Make the search more focused
Instead of searching for a tool that promises to solve an entire project, break the workflow into steps and identify the one that costs you the most time or requires a workaround. Then check whether the need is primarily about file handling, editing, visualization, modeling, simulation, or connecting to another tool. This narrows the search and makes it clearer what to try first.
When you find a candidate, consider where it fits into the workflow: Does it help bring data into SAMSON, work with the document, compute or update a model, display results, or move content back out? That question helps set practical expectations. An importer, for instance, addresses file parsing; it does not by itself provide a new simulation method. A visual model changes a representation, while an interaction model is involved in energies and forces.
Apps can be opened from Home > Apps or found using the Find everything search box at the top of SAMSON. Editors are accessed from the viewport’s left-side menu. Knowing these entry points makes it easier to try a new capability without interrupting your whole workflow.
When the missing tool does not exist
If you already have code or a specialized method, you may be able to integrate it rather than recreate it. The SAMSON SDK is used to develop extensions such as apps, editors, force fields, and services. Its code templates and development features are intended to support extension development, and SAMSON handles areas such as visualization and data management. The Developer Guide explains how to install the SDK and create or distribute an extension. For simpler automation inside SAMSON, the documentation also points to scripting as an alternative to building a compiled extension.
Extensions can also be distributed through SAMSON Connect. Developers can make them free or offer subscriptions, including different monthly or yearly tiers. That means a useful internal tool can potentially be shared with other users, while developers can choose how access is provided.
The practical takeaway: identify the exact step that is slowing you down, match it to an extension category, and look for a focused addition before redesigning the whole workflow. To explore the available options and development paths, learn more about extending SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.