Author: OneAngstrom

In molecular modeling, communicating structural details clearly is essential. Whether you’re preparing a presentation, documenting your work, or adding clarity to complex biomolecular arrangements, animation helps tell your story. Yet, there is a common bottleneck: how do you guide attention…

When comparing proteins, researchers often face the challenge of aligning only a specific region of interest — for instance, a conserved binding pocket or a particular structural motif — rather than the entire protein. This type of region-specific alignment can…

When setting up molecular dynamics (MD) simulations with pulling forces—especially center-of-mass (COM) pulling—one common but potentially problematic decision is defining the simulation box size. Selecting inappropriate box dimensions can interfere with the pulling process and compromise the reliability of results.…

Color is more than just aesthetics in molecular modeling. When examining complex biomolecular systems, color can reveal structural patterns, highlight molecular properties, or help detect issues hidden in raw structures. A common challenge for molecular modelers is choosing suitable color…

While SAMSON is continuously updated to improve performance and add features, some users—especially in academic or enterprise settings—might need to run a previous version to ensure compatibility with specific workflows, operating systems, or legacy extensions. If you’ve ever struggled to…

Molecular modelers often work in complex research environments where consistency and reproducibility are critical. In some cases, a team or a collaborator may still rely on an earlier version of a software tool. Or perhaps an older SAMSON Extension is…

One of the recurring challenges for molecular modelers working with SMILES files is identifying and isolating molecules that contain specific substructures. Searching by substructure matters—a lot—when you’re building small molecule libraries, designing focused chemical series, or preparing datasets for further…

Working with conformational pathways and molecular dynamics trajectories often requires efficient ways to visualize movement between structures or along predefined paths. Molecular modelers frequently face this need, whether to analyze results, showcase simulations, or communicate structural changes over time. To…

Molecular modelers often face the challenge of presenting complex atomic transitions and simulations in a clear and visual way. Whether you’re showcasing conformational changes, docking processes, or molecular dynamics, it’s helpful to create a visual trail that tracks how atoms…