Author: OneAngstrom

When working with molecular simulations in GROMACS, fine-tuning your index groups can unlock more targeted analysis, steering, and restraint strategies. However, knowing when to add these custom groups can make a big difference—especially if you want to avoid errors and…

When working with complex macromolecular structures, it can be challenging to distinguish overlapping elements or perceive spatial depth accurately. Whether you’re preparing a figure for publication or exploring a structure visually, the depth may seem flattened, making interpretation harder than…

Molecular structures can be highly intricate, often composed of thousands of atoms, bonds, and surfaces interweaving in dense formations. For researchers and molecular designers, interpreting such structures visually isn’t just helpful—it’s necessary. But even with advanced rendering tools, certain spatial…

Designing analogues and exploring chemical space are central tasks in molecular modeling and drug discovery. However, generating chemical libraries using conventional cheminformatics workflows can often be time-consuming and require custom scripting or external software tools. The Replace fragments feature of…

Switching between different molecular orientations and projections is a common—and sometimes frustrating—task in molecular modeling. Whether you’re aligning molecules, creating visuals, or inspecting specific structural features like active sites or crystal lattices, constantly rotating, zooming, and panning your model can…

When preparing molecular animations or presentations, a common issue many molecular modelers face is how to generate smooth, visually informative rotations around a structure. You want to highlight a molecular assembly from all angles, but manually moving the camera frame…

One of the most common frustrations molecular modelers face when analyzing molecular structures is the accidental loss of measurements between atoms. Whether you’re checking hydrogen bond lengths, backbone distances, or tracking how structures change during simulations, a single misclick can…

Creating compelling molecular animations is a key part of communicating scientific ideas, whether you’re presenting to colleagues, teaching a class, or publishing online. But just like in a good video or film, sometimes it’s all about the pause. A precise…