Molecular modeling professionals and enthusiasts often juggle a variety of tools, commands, and procedures to achieve their desired outcomes, which can sometimes be overwhelming and time-consuming. Imagine having an intelligent assistant that not only simplifies these tasks but also streamlines your workflow by executing them directly. Enter SAMSON AI, the intelligent assistant tailored for SAMSON, the integrative molecular design platform.
One of the most empowering features of SAMSON AI is its ability to understand and execute specialized commands. Let’s delve into how these can make your molecular modeling tasks more efficient and intuitive.
What Are SAMSON AI Commands?
SAMSON AI features a suite of commands designed for different aspects of molecular modeling. These commands let you trigger specific actions, generate Python scripts, select molecular structures, and much more—all through simple, natural language prompts. Below, we explore some of the most popular and impactful commands:
/do– Execute actions directly./script– Generate Python scripts for advanced functionality./select– Select specific molecular nodes with precision./learn– Absorb and understand information from external URLs or documents./refer– Ask questions based on previously learned information./forget– Reset by erasing all previously learned data.
Interested? Below, we dive deeper into how to use some of these commands effectively.
/do Command: Streamlined Execution
The /do command significantly cuts down the time you might spend manually performing simple or complex actions within the platform. With a single line of text, SAMSON AI can zoom to specific regions, apply models, change visual attributes, or perform advanced tasks.
For example, you can type:
/do zoom to the binding site./do select the ligand and apply a licorice model./do remove water.
This intuitive command lets you interact with the molecular scene faster and more fluidly, making it easier to focus on your analysis rather than repetitive operations. Take a look at the following visual example illustrating command usage:
/script Command: Unlock Python’s Potential
With the /script command, you can harness the power of Python to write scripts tailored to your specific workflows. Beyond simple actions, this command integrates SAMSON’s Python API with other Python libraries for tasks like machine learning or computational analyses.
For instance, you could input:
/script select all atoms and translate them in the z direction by 1 angstrom./script create a GUI that lets me enter a distance in angstrom, with a 'Move' button./script compute the gyration radius of the receptor.
This capability is especially valuable for researchers and developers seeking to combine molecular modeling with automation or custom applications.
/select Command: Precise Node Selection
Node selection is a frequent but often tedious task in molecular modeling. The /select command simplifies this by letting you describe structures or criteria in natural language. SAMSON AI then translates this into its Node Specification Language (NSL) and executes your request.
Consider these examples:
/select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
Even complex queries like identifying residues within proximity to specific molecules become quick and effortless with this feature.
Empower Your Workflow with Simple Commands
These are just a few highlights of what SAMSON AI commands can do. By integrating intelligence directly into your modeling environment, SAMSON AI allows you to shift focus from technical hurdles to insights and discoveries.
Learn more about SAMSON AI’s capabilities and explore other commands in the full documentation: https://documentation.samson-connect.net/users/latest/samson-ai/.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started with SAMSON today.