Author: OneAngstrom

When working with complex molecular models, color is much more than just aesthetics. It plays a critical role in distinguishing between atoms, molecules, conformations, and other elements of a model. An effective color palette can help make a visualization understandable…

When preparing molecular animations, one common challenge for researchers and educators is how to clearly communicate structural or mechanistic changes without overwhelming the viewer. Animations that show atoms or molecules vanishing abruptly or becoming transparent can cause confusion or visual…

When working in molecular modeling, complex manipulations are often made easier through specialized tools for selection, transformation, or even structure generation. In SAMSON, these tools are called Editors. If you’ve ever wondered why SAMSON allows only one Editor to be…

Running molecular dynamics (MD) simulations is time-consuming and often demands careful hardware usage—especially when working on a laptop or desktop that also serves other daily tasks. One of the challenges faced by molecular modelers using local GROMACS simulations is the…

In molecular modeling and structural biology, clear visual communication can be just as important as accuracy. When presenting molecular processes or dynamic events—whether in a team meeting, educational video, or scientific conference—there are moments when you want part of the…

When building molecular animations, sometimes showing less tells more. Whether you’re creating instructional visuals, presentations for collaborators, or just cleaning up a complex scene, being able to hide and reveal molecular components precisely between frames is essential. In SAMSON, that’s…

When preparing a molecular dynamics simulation involving center-of-mass (COM) pulling, one challenge that often arises is correctly sizing the simulation box. Too small, and you risk violating periodic boundary conditions; too large, and computational resources are unnecessarily wasted. This blog…

When working with molecular systems, storytelling isn’t just helpful—it’s essential. Whether you’re trying to communicate a complex biochemical process or guide someone through your model step by step, the way you present atoms and interactions makes all the difference. One…

When working on lead optimization or structure-activity relationship (SAR) studies, chemists often ask: what happens if I substitute this atom or group at a specific position in my molecule? Answering this question manually for many analogs can be a tedious…