A molecular structure can look ready for simulation while still containing details that complicate preparation: alternate atom locations, waters you do not intend to model, small molecules without available parameters, or ions that should be handled later. Removing everything that…

A molecular model can contain exactly the information you need and still be difficult to present. A wide view may show the overall complex but make an important interaction hard to see. A close-up can reveal that detail while leaving…

Starting a DNA nanostructure project often means solving two problems before the modeling begins: finding a design worth reusing and figuring out whether its file format fits the next step in your workflow. Rebuilding a published structure from scratch can…

Building a carbon nanotube by eye can be quick, but it can also leave you unsure whether you created the structure you intended. A small change in a mouse gesture may change the tube’s length, orientation, or radius. When you…

If you have ever paused in the middle of a molecular modeling task because you could not find the right panel, you are not alone. A viewport, structure tree, settings panel, action history, and animation controls can all compete for…

A production molecular dynamics run begins before the first simulation step. One frequent source of avoidable trouble is a shaky handoff from equilibration: the wrong input, parameters that no longer match the equilibrated system, or results that are imported in…

A molecular structure can contain thousands of atoms, several chains, and multiple kinds of information. When everything is shown in similar colors, it becomes difficult to tell one part from another—or to spot the property you meant to investigate. The…

A molecular structure can change substantially without any single local measurement telling the whole story. It may expand, collapse, or rearrange into a different overall shape. When you need a quick way to track that global size change across a…