When you are working on a molecular model, a task that takes only a few minutes can become a real burden when you have to repeat it across many structures or repeat it every time a project changes. Repeating the same steps also makes it harder to remember exactly what you did. A useful response is not necessarily to automate everything: it is to identify which parts of your work benefit from scripting, and which require a different capability.
SAMSON’s Scripting and Extending SAMSON guides offer two complementary routes. Scripting is the starting point for automation, reproducibility, and Python workflows inside SAMSON. Extending SAMSON is the route to explore when you want to install additional capabilities or learn about the Software Development Kit (SDK) and extension distribution.
Start by naming the repeated work
Before writing a script, describe the task in plain language. What do you repeat? What should be the same each time, and what changes from one run to another? This small bit of planning helps distinguish a suitable automation task from a task that needs a new capability.
- Repeated steps: If your goal is to automate work inside SAMSON, begin with the Scripting guide.
- A workflow you want to preserve: If you want a scripted workflow to be reproducible or embedded in a document, Scripting is also the relevant path.
- A missing capability: If you need to add capabilities or manage extensions, start with Extending SAMSON.
This is a practical way to avoid choosing a tool before you have defined the problem. It also keeps a project’s scope manageable: first make the existing workflow clearer, then decide whether scripting or an extension is the right next step.
Think about reproducibility before you automate
Automation is most useful when someone can understand what the workflow is meant to do and when it should be used. Write down the purpose of the workflow, the inputs it expects, and the result you are trying to obtain. If the task changes from project to project, note which parts vary. These notes do not replace a script, but they make it easier to create, review, and reuse one.
For a workflow that belongs with a particular document, consider whether embedding a script or app in that document fits your needs. This can help keep the scripted part of the work close to the material it supports. The documentation identifies document-embedded Python workflows as one of the reasons to start with Scripting; consult that guide for the actual SAMSON workflow rather than assuming every task should be packaged the same way.
Choose the smallest useful next step
You do not need to follow every section of the documentation. If you are not writing Python or embedding scripts, you can skip Scripting for now. If you only need built-in capabilities and are not managing extensions, you can skip Extending SAMSON. This is a helpful way to keep learning focused: follow the route that matches the problem in front of you.
Once you have a script-based workflow, the next destination depends on what you want to do with it. The documentation points to Simulate and analyze for scripted modeling, path generation, or analysis pipelines, and to Share and collaborate when you want to distribute scripted documents or collaborate around them. For deeper references and troubleshooting, continue to Reference and help.
The main takeaway: start with the repetitive task, then choose the path that fits it. Use Scripting to explore Python automation and document-embedded workflows; use Extending SAMSON when the goal is installing or developing capabilities. You can follow the complete overview in Automate and extend.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.