If you’re a molecular modeler navigating complex tasks, the advanced commands of SAMSON AI could be a game-changer. Designed to automate repetitive actions, generate scripts, and more, these tools simplify workflows and optimize productivity. Let’s explore how you can use these commands effectively and add efficiency to your molecular design process.
SAMSON AI Commands: Your Shortcut to Productivity
SAMSON AI comes with specialized commands that open up a world of advanced functionality. From executing actions within your documents to learning from external information, these commands are incredibly versatile. Here are the key commands you can use:
/do: Execute actions (e.g., “zoom”, “select”, or “change color”)./script: Generate Python scripts for complex automations./select: Make selections using natural language./learn: Absorb and utilize information from a URL or document./refer: Interrogate previously learned data./forget: Clear all previously retained information.
Simply type / in the Assistant’s input box to see the list of available commands within the interface—a helpful starting point to understand what SAMSON AI can do for you.
Streamline Actions with /do
The /do command is your key to quick action execution. It empowers SAMSON AI to perform tasks across your document automatically, saving you time and effort. For instance, you might want to zoom in on specific elements, apply visual models, or adjust colors. Some examples include:
/do zoom to the binding site./do select the ligand and apply a licorice model./do remove water.
The simplicity of asking SAMSON AI to perform intuitive actions makes it accessible even to users new to automation. Check out this image showing the different available commands:
Automate with Python via /script
For more complex tasks, the /script command lets you harness the SAMSON Python API. Whether it’s trajectory analysis, GUI creation, or machine learning integrations, this command brings the power of scripting to your designs. Here are some examples:
/script select all atoms and translate them in the z direction by 1 angstrom./script compute the gyration radius of the receptor./script create a GUI that lets me enter a distance in angstrom, with a 'Move' button.
The pre-built Python API support ensures that your scripts can interact seamlessly with SAMSON’s structure and data. If you’re ever stuck, SAMSON AI guides you with suggestions for coding queries.
Simplifying Selections with Natural Language
One of the most user-friendly features is the /select command. Rather than navigating intricate structures manually, you can simply describe what you want using everyday language:
/select the binding site./select all lysines in chain B./select all side chains within 5 angstrom of the ligand.
This command uses SAMSON’s Node Specification Language (NSL) to transform your input into precise selections and execute them. It’s a lifesaver when dealing with extensive molecular datasets.
Information From External Sources
The /learn and /refer commands are perfect for expanding SAMSON AI’s knowledge. Feed SAMSON AI URLs of research papers, articles, or documentation for instant context and integrate it into your project. For example:
/learn https://www.biorxiv.org/content/10.1101/2022.08.03.502585v2.full.pdf/refer Give me a table showing the IFR estimates per age group.
These capabilities make SAMSON AI an excellent assistant, one that learns alongside you and adapts to project needs.
Conclusion
The advanced commands of SAMSON AI simplify many aspects of molecular modeling, freeing you up to focus on innovative science rather than repetitive tasks. Whether you’re working with complex selections, automating workflows through Python, or learning from external data, these tools are designed to save you time and effort.
To dive deeper and see further details about these commands, visit the official SAMSON AI documentation page.
*Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at SAMSON Connect.