Author: OneAngstrom

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…

When studying molecular systems, understanding how a structure interacts with its environment, folds, or binds to other molecules can be a persistent challenge. A useful metric to tackle this problem is the Solvent-Accessible Surface Area (SASA). Whether you are analyzing…

Visualizing molecular structures with depth and clarity is crucial for molecular modelers, but sometimes flat 2D renderings can fail to provide an intuitive sense of depth. This is where SAMSON’s Ambient Occlusion settings can make a real difference in improving…

Protein modeling often requires comparing the structures of molecules to identify conserved residues, analyze conformations, or assist in downstream applications like homology modeling. However, aligning protein structures manually can be challenging and time-consuming—especially when precise superpositions are critical. SAMSON’s Protein…

For molecular modelers, understanding protein conformations and how they evolve along a path can be challenging. A vital tool to address this problem is the Ramachandran plot, which provides a clear visualization of protein backbone torsion angles (phi and psi).…

Molecular modelers often encounter a common challenge: how can you optimize specific regions of a molecule without affecting the rest of its structure? This is especially relevant when working on large molecules where only a local part of the system…