Author: OneAngstrom

Molecular animations are powerful tools for communicating complex structural and dynamic concepts. Whether you’re presenting a conformational change, a docking event, or an interactive walkthrough of biomolecular interactions, every frame matters. But there’s a challenge many molecular modelers face: giving…

Molecular modelers often deal with complex biomolecular systems made of long sequences of residues spanning multiple chains. One common challenge is maintaining clarity when switching between views: sequences, 3D models, and structural hierarchies. SAMSON addresses this issue with the Sequence…

Working with complex molecular systems involves not just visualization, but also managing the structure of the data. For molecular modelers, this can quickly become a challenge—especially when handling large protein assemblies, predictions from AlphaFold or Chai-1, or multiple working hypotheses…

When creating molecular animations, it’s often essential to trace the movement of atoms over time. Whether you’re demonstrating a docking process, simulating molecular dynamics, or showcasing the motion generated by a custom animation, documenting the precise trajectory can be critical…

When you’re creating a molecular animation in SAMSON, one challenge that can arise—often unexpectedly—is an unwanted change in camera perspective. You might spend a significant amount of time setting up a precise camera orientation for a particular frame, only to…

For molecular modelers, communication often hinges on the clarity and visual impact of shared images. Whether you’re crafting visuals for a publication, presentation, or collaboration, rendering realistic materials can be surprisingly time-consuming. Setting up each surface – glass, metal, or…

When working with complex molecular systems, it’s not always necessary (or desirable) to optimize the whole structure. Whether you’re fine-tuning a ligand inside a binding pocket or just adjusting a fragment of a large biomolecule, minimizing only a specific region…

Working with NMR-derived molecular structures often means handling NOE distance restraints that involve pseudoatoms—averaged positions typically used to represent equivalent hydrogen atoms. While helpful from an experimental perspective, pseudoatoms can become a bottleneck during structure refinement, especially when your modeling…