Author: OneAngstrom

When collaborating online or presenting research, molecular modelers often struggle with visibility. Whether it’s finding good collaborators or allowing others to explore your molecular simulations, having an online scientific presence can make a significant difference. In this post, we explore…

In molecular modeling, it’s often challenging to visually convey how a molecular structure moves or behaves, especially when presenting to interdisciplinary teams or students. Static images or even simple rotations might not fully capture local conformational changes or subtle rearrangements.…

When visualizing molecular models, clarity and interpretability are everything. If you’re working with large biomolecules or need to present complex data about structural attributes (like residue polarity or temperature factors), the way those attributes are color-mapped can make a big…

One common roadblock for many molecular modelers is the difficulty of integrating their own code or favorite external tools into larger modeling platforms. Maybe you’ve developed a docking routine in Python, or rely on a web-based prediction tool. Jumping between…

If you’ve ever needed to adjust only part of a molecular structure while keeping the rest fixed, you’re not alone. This situation arises frequently in structural biology, materials science, and computational chemistry. For example, when refining local geometries around a…

Molecular modelers often juggle multiple tools to simulate, visualize, or analyze molecular systems. One common frustration is having to manually install, update, or deactivate plug-ins or packages when testing new workflows or optimizing performance. If you use SAMSON, there’s a…

Writing scripts to analyze and manipulate molecular systems often requires both knowledge of a specific API and time spent debugging syntax errors. If you’re working with Python in SAMSON and find yourself switching between the documentation and your code editor…

If you’ve ever run umbrella sampling simulations and found yourself stuck at the next step—extracting the Potential of Mean Force (PMF)—you’re not alone. PMF profiles help interpret free energy landscapes, crucial in understanding molecular interactions, binding affinities, and conformational changes.…