A path can contain many energy values, but a plot of absolute energy is not always the easiest way to understand what is happening. If the values sit far above or below zero, the important changes along the path may…

You find an extension that looks useful, add it through SAMSON Connect, and then open SAMSON expecting to see a new tool. Nothing seems to have changed. Before adding it again or assuming it failed, work through a few checks:…

Starting a DNA nanostructure project from scratch can mean more than designing the shape: first you need a structure to work with, then a way to get it into your modeling environment, and finally a format that suits your next…

Few things interrupt a molecular modeling workflow like selecting a residue and discovering that you have also selected its backbone, side chain, or other related nodes. The problem is often not the selection itself, but the way the filter interprets…

You’ve arranged a molecular scene, added motion, and found a useful camera angle. Then you scrub to another frame—or export the movie—and the view has shifted. It’s a frustrating problem because the molecular motion may be correct while the story…

Building a nanotube from scratch can feel like a small task repeated far too many times: place a ring, position another one, check the spacing, and repeat. The hard part is not just making copies. The rings must be oriented…

A common frustration in molecular modeling is having two structures that represent the states you care about, but do not line up as ready-made endpoints for a transition-path calculation. The structures may differ in residue count, and a path generated…