For molecular modelers, efficiency is crucial. Whether analyzing complex molecular structures, preparing simulations, or refining atomic interactions, streamlining tasks can save valuable time and effort. With SAMSON AI, a powerful assistant integrated within the SAMSON molecular design platform, users gain access to a set of versatile commands that significantly enhance productivity.
Why Use SAMSON AI Commands?
Traditional molecular modeling workflows often require multiple steps, navigating through menus, and manual adjustments. SAMSON AI introduces a solution to this pain by enabling users to execute complex actions, generate custom scripts, and perform precise selections using simple natural language commands. This not only accelerates workflows but also reduces potential errors caused by manual operations.
Key Commands to Explore
The foundation of SAMSON AI lies in its specialized commands. Below, we highlight some of the most useful ones:
/do: Immediate Action Execution
The /do command lets you perform tasks directly in the interface. Whether it’s zooming in on specific regions, modifying visualizations, or cleaning up models, this command simplifies complex actions into straightforward instructions.
Examples:
/do zoom to the binding site./do remove water./do select the ligand and apply a licorice model.
For a quick overview, type / into the Assistant to see the list of available commands.
/script: Generating Python Scripts
SAMSON AI leverages the SAMSON Python API to let users automatically generate scripts for custom or repetitive tasks. This feature enables you to go beyond pre-defined actions and tailor solutions to your specific project needs.
Examples:
/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.
/select: Natural Language-Based Selections
The /select command transforms how you interact with molecular models by enabling precise, natural language-based selections. For example, selecting specific residues or groups within proximity of a ligand is as simple as typing a query.
Examples:
/select the binding site./select all side chains within 5 angstrom of the ligand./select all lysines in chain B.
Results are shown with a corresponding Node Specification Language expression, providing transparency and flexibility.
How to Get Started
Open SAMSON AI via Interface > Assistant or use the shortcut Ctrl + 0 on Windows/Linux and Cmd + 0 on macOS. Begin typing commands with / in the Assistant’s input box to unleash its potential.
To see the full documentation for all commands and examples, visit the official SAMSON AI documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at SAMSON Connect.