Molecular modeling requires precise tools to analyze structure and behavior. One common challenge for molecular modelers is tracking how a molecular system changes shape along a path or trajectory. Is the molecule becoming more elongated? How far is it from…

For molecular modelers, identifying accurate and meaningful transition paths between molecular states can be a pivotal step in understanding mechanisms such as ligand unbinding, protein folding, or any system involving transitions between energy minima. However, preliminary paths can often be…

If you’ve ever found it challenging to perceive depth in complex molecular models, you’re not alone. When studying intricate molecular structures, visually understanding the spatial relationships between different regions can be critical. Ambient occlusion is a rendering effect designed to…

For molecular modelers, visual clarity during presentations or analysis is essential. Whether you’re trying to highlight specific components, simplify a complex visualization, or create professional animations, controlling the transparency of elements like atoms, bonds, and meshes can make a significant…

Molecular modeling often requires a deep understanding of how structures deviate from idealized shapes, especially during simulations or along specific pathways. While measures such as radius of gyration are useful, they may not always capture the complexity of shape variations.…

Molecular modeling can be an intricate process, particularly when you have to switch between tools and editors to achieve the precision required in your workflows. For newcomers and seasoned users alike, navigating SAMSON's editor system effectively is a key to…

If you’re a molecular modeler dealing with complex simulations, you’ve probably faced challenges in implementing pulling simulations to study inter-molecular interactions or molecular dynamics. In this blog post, we’ll dive into the concept of center-of-mass (COM) pulling, a crucial simulation…