Author: OneAngstrom

Ever tried to present a complex molecular system, only to find that viewers get overwhelmed by all the atoms and bonds popping up at once? A common challenge in molecular modeling is not just building great models, but communicating them…

In molecular modeling, selecting specific residues in a large biomolecule can be tedious—especially when working directly in a dense 3D structure. Whether you’re prepping a simulation or trying to highlight particular regions, pixel-perfect clicking in the 3D Viewport just isn’t…

Before running advanced analyses such as ligand unbinding pathway searches or energy minimizations, it’s critical to properly prepare your molecular models. For many molecular modelers, skipping this step—or not doing it thoroughly—leads to frustrating errors during simulation, non-physical results, or…

One of the small but often frustrating challenges in molecular modeling with GROMACS is selecting the right input structure before running NVT equilibration. 🧬 It’s a critical step, but easy to overlook—especially if you’ve lost track of your project’s flow,…

When crafting molecular animations, timing plays a key role in ensuring your audience fully understands the processes being visualized. But sometimes, even the most carefully designed transitions go by too quickly, skipping right past a critical conformation or biological mechanism.…

As molecular modeling projects grow in complexity, keeping everything organized—especially when dealing with multiple structures, simulations, and annotations—can become a real challenge. Mistakenly overwriting an important molecule, struggling to recall how a selection was made, or navigating through scattered files…

When preparing molecular presentations, one challenge commonly faced by modelers is how to add dynamic motion to a static selection of atoms without overly distorting the system or distracting from molecular features. A static model can feel lifeless, but too…

When analyzing protein conformational transitions, visualizing the path is just one step in the process. For publication, presentation, or further computational treatment, you often need to export the results, including the series of conformations along a transition path and key…

When modeling complex molecular systems, precise manipulation of structures is key. Whether you’re arranging ligands, adjusting dihedrals, or preparing a visual output, simple grab-and-drag operations often aren’t enough. Many modelers struggle with getting molecules to move exactly how they want—often…

If you’re a molecular modeler using SAMSON, chances are you’ve encountered various SAMSON Extensions—modules that enhance your modeling capabilities. But as your workflow evolves, managing these extensions can become a challenge: Which are free? How do I try a paid…