Author: OneAngstrom

For many researchers and developers working in molecular modeling, one of the main challenges is integrating custom algorithms or tools with existing visualization and simulation environments. Often, researchers have developed their own code (for structure analysis, energy calculations, or custom…

When preparing molecular animations or presentations, it’s often important to convey structural dynamics in a clear and intuitive way. A common need is to rotate a specific part of a molecule—like a ligand, domain, or fragment—around its own center, rather…

Designing a focused library of compounds is a central part of molecular modeling, whether for virtual screening, SAR studies, or lead optimization. However, creating diverse analogues by hand can become tedious, especially when you’re tweaking only specific fragments. The SMILES…

For molecular modelers working on drug discovery or molecule optimization, building a focused library of analogues is a routine—but often tedious—task. Whether you’re performing lead optimization or investigating SAR, repeatedly modifying specific functional groups in a base structure can be…

When working on complex molecular systems, constantly switching between different parts of your model can slow you down. Molecular modelers often find themselves selecting the same residues, chains, or ligands over and over — whether for visualization, simulation, or structural…

When presenting molecular models, clarity and elegance go hand in hand. But if you’ve ever tried to represent dynamic states—highlighting or fading specific parts of a complex structure over time—you’ve likely wondered how to do this smoothly and repeatedly without…

When creating molecular visualizations, subtle camera movements can make a huge difference in effectively communicating key insights. A common challenge is to zoom into a molecular system while keeping the target point fixed—so that special effects like fog or depth-of-field…

One of the common frustrations faced by researchers, educators, and students in molecular modeling is running into IT restrictions when trying to install software—especially in shared environments or institutional systems. If you’ve ever struggled with needing administrator rights to install…

When working on molecular modeling projects, especially those involving proteins or nucleic acids, one frequent task is to simulate structural flexibility and then extract useful conformations. After exploring different conformations through normal mode analysis (NMA), many researchers hit a familiar…