A molecular modeling workflow rarely breaks because of one dramatic problem. More often, it slows down at a familiar bottleneck: a file needs a parser, a repetitive task needs automation, a structure needs a specialized visualization, or a simulation needs a model that is not part of the current setup.
When that happens, it can be tempting to look for one large tool that does everything. In SAMSON, a more practical first step is to identify the specific job you need done and match it to the kind of extension that provides that capability. Extensions are modules added through SAMSON Connect, and they can provide different components for working with molecular documents.
Start with the task, not the tool
If the pain is getting data into or out of a project, look for an importer or exporter. Importers parse files; exporters write document content to files. For example, the documentation gives PDB and XYZ as examples of formats that may be handled by these extensions. This distinction is useful when diagnosing a workflow: importing a structure and exporting a result are separate needs, even if both involve files.
If you need a new way to interact with a document, consider an editor. Editors respond to user input such as mouse and keyboard events, and can provide tools for tasks such as selecting regions, generating a nanotube, deforming a structure while preserving local rigidity, or applying a rigid-body transform. Editors are accessed from the left-side menu of the viewport.
If you need a particular function or connection to another tool, an app may be relevant. Apps can connect to an external executable or web service, integrate existing code with SAMSON, or provide new functionality. To launch one, use Home > Apps or search for it in the Find everything box.
For modeling and simulation, the relevant extension may be a model or state updater. Interaction models calculate energies and forces; examples in the documentation include spring, elastic network, and extended Hückel models. State updaters advance states during simulations and may implement minimization, Monte Carlo, or molecular dynamics methods. Visual models address a different need: how information appears in the viewport, such as a secondary-structure representation or an electron-density isosurface.
A simple way to choose
- Name the bottleneck. Is the issue reading or writing a file, editing a structure, visualizing a result, calculating forces, advancing a simulation, or connecting to another service?
- Match it to an extension family. Use the categories above as a starting point, rather than searching only for a broad description of your project.
- Check the Marketplace. Sign in to SAMSON Connect and browse its Marketplace to choose extensions. SAMSON downloads a default set of extensions the first time it starts; you can add or remove extensions later.
- Find and launch the tool. Apps can be opened through Home > Apps or the Find everything search box. Editors are available from the viewport’s left-side menu.
This approach helps separate a missing capability from a setup problem. For example, if a file will not open, first ask whether the required importer is available. If a structure can be loaded but is difficult to inspect, the need may instead be a visual model. The right category narrows the search without assuming that every extension works the same way.
When the exact tool does not exist
If the Marketplace does not cover your need, there are two documented routes to consider. For automation inside SAMSON without creating a compiled extension, the scripting resources are a useful next step. For a more integrated tool, the SAMSON SDK is available from the Download page after signing in to SAMSON Connect. It supports creating extensions such as apps, editors, force fields, and services, and includes code templates intended to help developers get started.
Building is not the only possible outcome. A developer can distribute an extension through SAMSON Connect, make it free or offer subscriptions, and configure subscription tiers. The documentation also describes selling access to cloud computing services from SAMSON. This can be relevant when a team has developed a specialized capability and wants others to use it.
The useful takeaway is to treat an extension as a targeted answer to a workflow need. First identify where work is getting stuck, then look for the matching extension type, and only consider scripting or SDK development if the available tools do not fit. For installation, development, and Marketplace details, see the SAMSON Extensions documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.