If you’ve worked on large or multi-step molecular modeling projects, you’ve probably faced the challenge of managing complex structures, reference files, scripts, and various annotations — all within a single workspace. Managing molecular data can quickly become overwhelming when everything…

When you’re building complex molecular models, visuals matter. Whether it’s distinguishing between different protein chains, highlighting interaction sites, or simply making your work look more readable and aesthetically pleasing, choosing the right color palette can make a big difference. Color…

When creating molecular animations for presentations, publications, or educational videos, one of the simplest but often underestimated challenges is managing which elements of the model the audience sees — and when. If you’ve ever wanted to reveal specific molecules or…

Molecular modelers frequently need to construct specific chemical structures not readily available in molecular libraries. Whether you’re reproducing a model from a journal article or exploring new chemical scaffolds, building molecules atom by atom is often a key part of…

Many molecular modelers using GROMACS have run into this: you want to track or manipulate a specific set of atoms during a simulation—maybe the side chains of neutral amino acids or every non-C-alpha atom in a protein. But GROMACS only…

When running molecular dynamics (MD) simulations, especially those that take time to compute, a common frustration among molecular modelers is not being able to track progress easily without interrupting their workflow. Whether you’re testing new force field parameters, prepping simulations…