Creating compelling molecular presentations isn’t just about pretty graphics — it’s about telling a story. Molecular modelers often struggle with managing the visibility of atoms, molecules or entire structures over time, especially during animated timelines where some structures need to…

For molecular modelers, repetitive tasks like removing solvent molecules, generating molecular surfaces, or adjusting visual styles are a constant part of the workflow. Traditionally, these actions require navigating through multiple menus in a complex interface. Over time, this can be…

When you prepare molecular animations to explain your research or present your findings, the clarity of visualization often makes the difference between confusion and understanding. A common challenge faced by many molecular modelers is: how to intuitively highlight structural features…

When creating molecular animations, researchers and educators often want to visualize how specific regions of a molecule or molecular system behave over time. However, a common frustration is trying to keep the camera focused on a particular region without having…

Preparing protein conformations properly is a necessary step before computing transition paths between them. However, it is often a source of frustration for molecular modelers. Missing atoms, inconsistent residue numbering, or incompatible PDB files can all lead to failed simulations…

Anyone who’s worked with GROMACS knows how essential index groups are when setting up complex molecular dynamics simulations. Whether you’re pulling a specific domain during umbrella sampling or analyzing RMSD for specific atoms, you typically need to create custom index…

Running molecular dynamics (MD) simulations is just one part of the journey. Once a simulation finishes, many researchers face a more frustrating step: importing and analyzing the results. This is especially true when working with multi-step workflows like those used…