A molecular modeling workflow rarely stays confined to one task. You may need to inspect a structure, prepare it for another program, apply a particular visual representation, or run a specialized calculation. When the capability you need is not part of your current setup, the practical question is: do you have to change your whole workflow, or can you add just the missing piece?
In SAMSON, additional capabilities are provided by SAMSON Extensions: modules that you can add to the platform through SAMSON Connect. Extensions can support different parts of a modeling workflow, from importing and exporting files to editing structures, visualizing results, and performing modeling or simulation tasks.
Start with the task that is slowing you down
It helps to describe the problem in terms of what you need to do, rather than looking for a tool by name. For example: “I need to parse this kind of file,” “I want to interactively modify the structure,” or “I need a visual representation for this data.” That description points toward the kind of extension to look for.
- Need to read or write a file? Importers parse files into SAMSON; exporters save document content to files. The documentation gives PDB and electron-density parsers as importer examples, and PDB and XYZ exporters as exporter examples.
- Need to interact with a document? Editors respond to user events such as mouse and keyboard input. Examples include selection tools, a nanotube generator, and tools for deforming structures or applying rigid-body transformations.
- Need a particular view? Visual models provide representations in the viewport. Examples include protein secondary structure, electron-density isosurfaces, and volume rendering of an electrostatics field.
- Need energies, forces, or simulation steps? Interaction models compute energies and forces; state updaters advance states during simulations. The documented examples include spring and elastic network models, minimization algorithms, Monte Carlo methods, and molecular dynamics algorithms.
- Need a broader capability? Apps can provide many types of functionality, including connections to external executables or web services and integration of existing code.
This distinction is useful because extensions are not all the same kind of tool. An editor changes how you work with a document; an importer or exporter handles file exchange; and a model may contribute to visualization or computation. Identifying the job first can make it easier to narrow your search.
Add only what your workflow needs
The first time SAMSON starts, it downloads a set of extensions included by default. You can add or remove others by signing in to SAMSON Connect and selecting extensions in its Marketplace. Once an app is available, you can start it from Home > Apps or find it using the Find everything search box. Editors are available from the left-side menu of the viewport.
A simple way to evaluate a possible addition is to ask three questions: What exact step will it help with? Is it an app, editor, importer, exporter, visual model, interaction model, or state updater? Where will you access it once it is installed? These questions help connect the extension’s role to the actual task, instead of adding tools without a clear use.
When the tool you need does not exist yet
If an available extension does not cover your use case, SAMSON also supports developing extensions with its SDK. The SDK can be used to create apps, editors, force fields, and services, and provides code templates and features intended to support development. The developer documentation covers installing the SDK and creating or distributing an extension. This can be relevant when you want to integrate existing code or build a capability specific to your work.
Extensions can also be distributed through SAMSON Connect. Developers can offer them for free or sell subscriptions, including different monthly or yearly tiers. That means a specialized tool can be shared with other users rather than remaining confined to one local workflow.
The useful takeaway is to treat an extension as a targeted answer to a workflow need: identify the missing step, find the extension category that matches it, and then add or develop the capability that fits. To learn more, see the SAMSON Extensions documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.