A molecular modeling workflow rarely has just one bottleneck. You may need to read a particular file format, create or edit a structure, apply a model, or inspect results in a more useful way. The frustrating part is that a useful capability may live in a separate tool—or may not be part of your current setup at all.
SAMSON addresses this through extensions: modules that add capabilities to the platform. Rather than treating an extension as one specific kind of software, it helps to think of extensions as a way to fill different gaps in a workflow. The right starting point is to identify what is slowing you down, then look for the extension type that matches that task.
Match the bottleneck to the extension
- Need to bring data in or send it out? Importers parse files into a SAMSON document; exporters write document content to files. For example, the documentation describes PDB and electron-density parsers, as well as PDB and XYZ exporters.
- Need a more direct way to edit a model? Editors respond to mouse and keyboard events. Examples include selection tools, nanotube generators, structure-deformation tools, and tools for applying rigid-body transformations.
- Need a new way to see a result? Visual models provide representations in the viewport, such as secondary-structure views, electron-density isosurfaces, or volume renderings of electrostatics fields.
- Need calculations or simulations? Interaction models compute energies and forces, while state updaters advance states during simulations. The documented examples include spring and elastic-network models, and minimization, Monte Carlo, and molecular-dynamics methods.
- Need to connect existing software or add a broader capability? An app can connect to an external executable or web service, wrap existing code, or provide new functionality.
This categorization is useful because it turns “I need a better workflow” into a more specific question: Is the friction in file handling, interaction, visualization, calculation, or integration? A specific problem is easier to search for than a general request for a new tool.
Try an extension before rebuilding your workflow
SAMSON includes a set of extensions that are downloaded the first time you start the platform. If you need more, sign in to SAMSON Connect and browse the Marketplace. After adding an extension, apps can be opened from Home > Apps or found with the Find everything search box. Editors are available from the left-side menu of the viewport.
A practical way to evaluate a candidate extension is to connect it to one real task you already perform. Check whether it addresses the specific bottleneck, whether it works with the type of content you need, and whether it fits into the rest of your process. This keeps the decision grounded in your work rather than in a long list of features.
When the missing tool is your own
If no available extension fits, SAMSON can also be extended by developers. The SAMSON SDK is available from the Download page after signing in to SAMSON Connect. It supports building extensions such as apps and editors, with code templates and tools intended to help development. The platform can handle visualization and data management, while an extension focuses on the developer’s particular functionality.
Developed extensions can be distributed through SAMSON Connect. The documentation describes options to make extensions free or offer subscriptions, including monthly and yearly tiers. For details on creating and distributing an extension, see the Developer Guide.
The larger takeaway is simple: when a molecular workflow feels constrained, first identify the kind of task that is getting in the way. An importer, editor, visual model, interaction model, state updater, or app may address that need without requiring you to replace everything else in your process.
Learn more about extending SAMSON.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.