When setting up molecular simulations, particularly those using periodic boundary conditions (PBC), understanding and applying the minimum image convention is crucial. This principle ensures that your system behaves realistically during simulations by avoiding unintended interactions between a molecule and its…

For molecular modelers working with SAMSON, organizing and identifying nodes effectively is an essential part of the workflow. This is where the Node Specification Language (NSL) comes into play, allowing users to specify and query attributes of nodes such as…

In molecular modeling, one of the recurring challenges is the need to adjust or manipulate structural assemblies, particularly when working with docked atoms or meshes. If you’ve ever been in a situation where you needed to undock molecular structures efficiently,…

One of the prominent challenges molecular modelers often face is understanding how proteins interact and organize in their environments. Whether it’s deciphering crystal structures or biological assemblies, the arrangement of proteins plays a crucial role in modeling workflows, simulations, and…

Have you ever wanted to keep your focus on a specific group of atoms while observing a molecular simulation, without losing your carefully set camera angle? The ‘Look at atoms’ animation in SAMSON provides an elegant solution to this common…

Molecular modelers often face the challenge of visualizing and manipulating molecular structures dynamically. One of the hardest aspects can be efficiently moving groups of atoms or meshes out of their docked positions, especially when working on presentations or better understanding…

As a molecular modeler, have you ever worked on a project where selectively hiding parts of a molecular structure could make your presentation more effective or your analysis more precise? Whether you’re preparing an insightful animation for your research or…

In molecular modeling, presenting complex simulations effectively to collaborators or supervisors is key. However, showing only the relevant parts of a molecular structure at the right moment during animations can be challenging. If you’ve been struggling with creating seamless and…