When preparing molecular animations in SAMSON, one of the common challenges is managing the visibility of complex molecular structures throughout the timeline. For example, you may want to emphasize a particular molecular subunit by momentarily hiding others, or gradually simplify…

If you’ve been trying to generate smooth transitions between protein conformations using interpolation tools and keep running into frustrating errors like: “Cannot proceed because the structure does not make one connected component,” you are not alone. This issue is a…

When working with complex molecular systems, it’s common to want fine control over what parts of a structure are optimized. Imagine you’re refining only a flexible loop in a protein, or adjusting a ligand’s conformation while keeping the binding site…

When working with protein models, it’s not uncommon to encounter residues adopting unfavorable conformations. These outliers can emerge during homology modeling, loop building, or even after seemingly successful refinements. Spotting and correcting them efficiently is crucial for improving model quality…

Creating presentations or videos to showcase molecular simulations and structures often comes with a frustrating problem: how to show the right parts, guide the viewpoint fluently, and highlight molecular features clearly. Static images leave too much to interpretation, and manual…

One of the key challenges in performing Umbrella Sampling simulations is selecting meaningful initial conformations. Researchers often face this question: how should I extract configurations from my GROMACS trajectory in a way that ensures smooth sampling along the reaction coordinate,…